Perfect Layout: Settings Expressions DO First Optimize Reset/Hide MMRests Chords Groups Alignment Layers/Cues Tuplets Express. Artics. Hairpins Slurs/Ties Counting Systems General
The silver edition has no expression tab.
To get the best results with the Perfect Layout plug-in it's important to use Finale®'s expression categories correctly.
The same goes for Finale®'s other default categories:
1.) Dynamics/Niente Circle: Keep dynamics only in a category with the keyword "Dynamics" (or Dynamik or dynamiques or dinamiche from the international editions of Finale). It's also possible to combine words like "Percussion dynamics" or "Above Staff Dynamics" - as long as the main keyword is found.
2.) Expressive Text: Expressive text expressions are partially taken into account in alignment. Especially in combination with dynamics or hairpins on the same measure position the expression will be aligned horizontally and/or vertically.
3.) Rehearsal Marks/Tempo Marks/Tempo Alterations: Elements in these categories are taken into account for vertical and horizontal alignment above the staff. Rehearsal Marks can also be placed at different positions at the beginning of a staff (see alignment tab).
4.) Technique Text: Expressions in this category are not vertically/horizontally aligned!
5.) "Cue"-Keyword (user-defined): see Layer/Cues tab.
6.) "In Parts Only"-Keyword (user-defined): see Reset/Hide tab.

If you use expressions with numbers only, the plug-in can move them into the Rehearsal Marks category, if these options are checked. Numbers with rectangular expressions can be automatically moved (Option "Move Number Expressions with Non-Circular Enclosure to Rehearsal Mark Category"). Numbers with circular enclosures are typically fingerings and will not be moved automatically.
Measure number expressions can also be moved automatically: the plug-in compares the expression number with the measure that the expression is used in and if it fits, it will be moved (Option "Move Measure Number Expressions to Rehearsal Marks Category").

Note 1:
For best alignment use as less expressions in one measure position as possible.
E.g. "più f" or "pp sub." should be a single expression. The horizontal alignment (not centered as in standard dynamics, but left- or right-aligned) is automatically applied in these cases.
The same goes for tempo marks and rehearsal texts:
If you have for example the four above staff lines "M" (=Letter M), "Andante", "q=100" and "Verse" don't use four expressions on top of each other, but only two: use the rehearsal mark M plus a single expression for the text.
The Perfect Layout plug-in has a few cases where multiple expressions are aligned correctly, but it becomes difficult if it is more than two of the same type.

Note 2:
If you have imported a document through MusicXML, it performs an automatic category assignment if the whole score is processed with the Perfect Layout plug-in: If the plug-in detects typical keywords, it suggests to move the expressions to the corresponding category.
This works very good with dynamic expressions and also with a few standard expressions from the other categories. But especially if you use less common or foreign texts, the automatic category detection does not work. In this case it is important that you move the expressions to the correct category before applying the plug-in. Otherwise not all features will work.
You can remove the opaque background from rehearsal and tempo marks/alterations with the option "Remove 'Opaque' from Reh./Tempo Marks".
Usually the opaque feature is not required for rehearsal marks after applying Perfect Layout, as the plug-in will remove all collisions anyway. Nevertheless it's possible to fine-tune this feature by the selection list which includes
"Don't Remove",
"Remove If Most Expressions Are Opaque" and
"Always Remove".
If the lowest element on a measure or staff is above the lowest baseline, the dynamic expressions can be shifted upwards (Option: "Shift Dyn. Epxressions Up by XXX If Lowest Element is Staff Line"). By default Perfect Layout will search the whole system for the lowest element. If "For Lowest Element Only Look at Expression's Measure" is selected, it will only analyze the measure of the expression for the lowest element.

Also check "Alignment->Align Dynamic Expressions Only If Connected by Hairpins". If this is not activated (which is by default in parts), it may lead to dynamics being vertically aligned which override the "Shift up" value.

Image 1:
Left Measure: Default placement of dynamics at baseline
Right Measure: "Shift up by 6 EVPU" and "For Lowest Element Only Look at Expression's Measure" activated
You can set the vertical distance of dynamic expressions to many other notation elements.
To optimize the look some dynamic symbols (mf, sf, rf, f) can get reduced offsets which better fits their skyline.
You can set the vertical distance of expressive text expressions to slurs and ties.