The Perfect Layout has two algorithms for placement of tempo and rehearsal expressions above the staff:
a.) Align each expressions individually (closest to the staff)
b.) Align all expressions per system on the line of best fit (above all other objects)
c.) Align all text expressions on the line of best fit, but keep rehearsal marks close to the staff (Option "Per System/Skip Rehearsal Marks")

This option can selected differently for the score and the parts.
Individual alignment gives more vertical space for other objects and works better in narrow part pages. Alignment per system is usually better readable, but requires more space.

Image 1:
Top (a): Individual alignment (close to the note/staff)
Middle (b): Alignment on the best line of best fit
Bottom (c): Alignment of the text expressions. Rehearsal marks are close to the notes/staff.
If you add the word ABOVECHORD to the description field of an expression or the name of an expression category in Perfect Layout v3+, it will place the expression above chord symbols or even above other "normal" expressions.
On top are still always tempo and rehearsal marks.
"Normal" expressions (i.e. no ABOVECHORD tag and not rehearsal or tempo expressions) are always placed below chord symbols.
Like this it's easy to generate a vertical priority of four symbols:

Image 2: The ABOVECHORD tag

Still it's highly recommended to use multi-line expressions if you want rehearsal/tempo marks that span multiple lines vertically aligned in a user-defined way.
The same goes for wide horizontal tempo marks:
Don't put "Allegro" and the tempo mark "q=120" into two separate expressions, but use them in one expression.

You can download the test file used in the image above to check the expressions settings.
Some general options for expression, articulation and hairpin alignment can be set on this tab:
An "Extra Vertical Collision Offset" can be set here (Default: 5 EVPU). This value is added to all vertical offsets on the expression, articulation and hairpin tab and makes it easy to generally increase the vertical distances of two objects. Don't forget to also adjust the "Below Staff Baseline Position" and/or the "Vertical Entry Offset" on the "Optimize" tab in order to adjust the general placement of dynamics and expressive text.
The Silver edition has eight predefined values (-9, -6, -3, 0, 5, 10, 15 or 20 EVPU), while the Gold edition is fully flexible.

Image 3: Extra Vertical Collision Offset: -2, +5 and +15 EVPU
Note: If there is enough space before the fff in measure 1 and the fff would be placed below the "Express.->Very Low Note Threshold Below Staff Line" value, Perfect Layout will automatically move it before the first note (not below).

The "Harmonize Offsets and Aligment of Rehearsal and Tempo Marks" option harmonizes the offsets in the Rehearsal Marks, Tempo Marks and Tempo Alteration categories which improves their horizontal and vertical alignment.

The overall vertical alignment of hairpins, dynamics and expressive text on a system is done in a complex algorithm which takes into account many vertical and horizontal positions and distances and tries to create a visually balanced and pleasing look.
The options for the algorithm are:
a.) Vertically Align Dynamic Expressions Only If Connected by Hairpins: self-explanatory (see image 4 below)
b.) Even out Vertical Alignment of Hairpins and Dynamic Expressions: If selected, the vertical alignment algorithm is run twice. This usually leads to more hairpins and dynamics being on the same vertical position and thus look smoother.

In the parts where there is usually more vertical space available and where readability is much improved by dynamics and hairpins being on the same vertical position, it makes sense to align close dynamics also if unconnected and to even out the vertical alignment.
In the score these options usually are selected the other way round. These are also the default settings.
Single dynamics on very low notes are usually not taken into account for overall vertical alignment (see the fff and the ff in image 3 above).

Image 4:
Top: All dynamics are aligned, also if unconnected.
Bottom: Only those dynamics are aligned that are connected by a hairpin.

While dynamics and hairpins and single staves are aligned with a certain distance to the lowest object above them, on two staff groups like in piano notation they are usually centered between the lowest object from above and the highest object from below. As is single staves they still have to be connected to adjacent dynamics/hairpins in a musical and visually balanced way.
The Perfect Layout offers vertically staff-centered alignment of dynamics and hairpins in combination with automatic best staff distance calculation.
To activate this feature check "Center Dynamics and Hairpins Between Two-Staff Groups".
The feature is still in beta state, but already delivers very good results most of the time - even if there is not much vertical space available.
In order to avoid collisions of rehearsal marks and measure numbers, you can easily select their placement in "Place Rehearsal Marks at Start of System" and "Place Measure Numbers at Start of System". Of course, it is also possible to keep the original position.
Don't forget to uncheck "Hide Measure Numbers" in the rehearsal mark expression to actually see measure numbers next to rehearsal marks.
To fine-tune the placement of measure numbers, you can also change the horizontal and vertical offsets at system start manually. By default these values are created automatically ("Automatically Set Measure Number Offsets at Start of System").

To avoid collisions with group brackets, you can check "Extra Vertical Offset for Curved Group Brackets". It moves measure numbers on top of a group bracket slightly upwards and below the bracket slightly downwards.

Image 5: Extra vertical offset for curved group brackets

Note: If you have a score with linked parts, you need at least Finale 27.3 to make full use of all measure number placement features of Perfect Layout.
Previous Finale versions didn't allow individual placement of measure numbers in all linked parts through plug-ins.

In general it is recommended to use narrow fonts for measure numbers at system start (e.g. Arial Narrow) - especially when the piece has more than 100 measures (i.e. 3 digits). Other recommended serif fonts for measure numbers are available here.

Here are some of the options:

Image 6:
1: Reh.Mark: Left Edge, Left-Aligned   /   Measure Number: Left Edge, Left-Aligned, Above
2: Reh.Mark: Left Edge, Centered   /   Measure Number: Centered over Clef
3: Reh.Mark: Centered over Clef   /   Measure Number: Left Edge, Right-Aligned, Below
4: Reh.Mark: Centered over Time-Signature   /   Measure Number: Centered over Clef
Other options are "At Music Start" and "After Time Signature".
Perfect Layout v3+ can do a few auto-corrections on measure numbers below the staff that collide with other objects.

a) Measure numbers below the barline are shifted down when colliding with ties or slurs that span from the previous measure to next measure (see image 7).
If the measure number has to be shifted very low (more than 35 EVPU), then the distance to the colliding object will be reduced by 6 EVPU. The maximum distance that the measure number will be shifted down is 23 plus the selected offset (14 EVPU by default) plus the "Extra Collision Offset" (5 EVPU by default) resulting 23+14+5-6=36 EVPU by default.

If the default placement of your measure numbers below barline is as in image 7, you will have hardly any collisions with measure numbers when using the "Loose Spacing" preset in Perfect Layout.

Image 7: Shifting colliding measure numbers down (m.22, m.30) or deciding to maintain their placement (m.68)

b) Measure numbers in the score on each measure below the bottom staff are shifted down when colliding with symbols (see image 8). This is done consistently over the whole score: they will all get the new vertical distance.

In the Gold edition the distance can be adjusted with the option "Alignment->Measuren Numbers->On Collisions with Other Objects Below Bottom Staff Shift Down by" plus the value of "Alignment->Extra Collision Offset".
In the Silver edition the distance is only handled indirectly with the "Alignment->Extra Collision Offset" value. The default distance is 19 EVPU (=14 EVPU Vert. Distance + 5 EVPU Extra Offset).

Note: if there is no collision because the measure numbers are already very far below the staff, then they will keep their position. They will not be shifted upwards.

Image 8: Vertical alignment of measure numbers below staff
Perfect Layout supports automatic vertical alignment of lyrics below the staff in relation to the lowest notes, articulations, slurs or ties.
Tuplet brackets on lyric staves are automatically shifted onto the top of the staff to avoid collisions (measure 1).

Some best practices:
-Make sure to have your lyrics aligned below the staff where you want to have them placed: i.e. not above the staff and not below another staff.
Use the Finale lyrics baseline to move the lyrics below the staff.
-If possible, reduce the number of lyrics verses to a minimum. If Perfect Layout has to align multiple verses, the order of the verses must be clear.
I.e. avoid verse 1 being the top lyrics line in the first system, but the bottom lyrics line in the second system.
-For best ledgibility it is recommended to place any dynamics on lyrics above the staff.

If you have two (or more) lyrics staves and the dynamics are valid for both staves, you can also place them below the lyrics of the top staff together with hairpins.
In this case make sure to set the hairpin alignment to "Move Hairpins Below Lyrics" (see below)

It is not recommended, but also possible to place the dynamics left to the notes, but above the lyrics. But this may already be difficult to read and can easily lead to collisions which Perfect Layout will not handle.

The adjustable vertical distance options are:
Vertical Distance to Lowest Note
Distance Between Multiple Lyrics Lines
Distance to Bottom Staff Line
(if all notes are only above the bottom staff line)

If you have hairpins below the staff, there are also four options for handling lyrics collisions with hairpins:
1.) Keep HP Position / Allow Collision with Lyrics
2.) Keep HP Position / Move Lyrics Down
3.) Move Hairpins Below Lyrics
4.) Move Hairpins Below Notes
On the Perfect Layout Gold version these options are available on the Hairpins tab.

Image 9: Automatic Multi-Verse Alignment with the Perfect Layout Plugin
Perfect Layout can do a few auto-corrections on horizontal accidental placement with the option "Horizontal Alignment of Multiple Accidentals":
a.) Accidentals are moved closer together if there is sufficient vertical space. This depends on the accidental shape and also included parentheses (Image 11).
The amount of overlap can be controlled with "Horizontal Distance of Several Non-Colliding of Parenthesized Accidentals".
b.) Gaps between notes and accidentals on chords with seconds will be reduced (Image 12 - supported from Perfect Layout v2.42)

Make sure to have "Accidentals->Use cross-layer accidental positioning" in Finale's document options activated (see Quickstart: How to use).
In PL v3/RGP Lua Accidentals->Use cross-layer accidental positioning is automatically activated.

Image 11: Overlapping accidentals

Image 12: Reduced gaps on chords with seconds