In general the Perfect Layout aligns
  • dynamic and expressive text expressions below the staff horizontally and vertically
  • tempo and rehearsal marks and tempo alterations above the staff horizontally and vertically
  • leaves all other expressions untouched.

Usually the plug-in first removes any manual adjustments, then looks for collisions and, should it detect any, moves the expression away from the colliding object.
If the horizontal offsets of the expressions are huge, then it is unlikely that a clear zero position was intended by the engraver. In this case manual (horizontal) adjustments are not removed.
The thresholds for "huge offsets" can be set in "Reset Horizontal Position of Dynamics Until Maximum Horizontal Offset" and "dito., Max. Horizontal Resset Offset for Whole or Dotted Notes".

Dynamic expressions in staves with lyrics are very often placed above the staff, these are currently not taken into account for alignment.
The option "Reset Vertical Position of Dynamics and Expressive Text on Notes With Lyrics" is switched off by default. If selected, dynamics above the staff will suddenly appear below the staff line if they were taken from the default dynamics category and it is still set to below baseline.

Some expressions usually only appear in the parts, to not mess up the conductor's score. These expressions must be placed in a user-defined category containing the keywords defined in "Hide Expressions in Score with Category Keyword(s)".
E.g. if you name the expression category "In Parts Only" and enter the keywords "part,only", then the plug-in will hide all expressions from categories with names that includes these keywords.

Image 1: Category "In Parts Only"

Just as expressions articulations positions are usually first set to the vertical default position and then tested for collisions.
It is highly recommended to keep the option "Reset Vertical Position of Note Articulations, Fermatas, Bows and Ornaments" selected.
Only recognized articulations are reset, i.e. shape articulations or articulations with unknown music symbols are not reset, except for those shape articulations that are explicitly defined in the Perfect Layout settings (e.g. up/down bow shape articulation).
Articulations that are usually aligned manually (e.g. arpeggio) are not reset by default (see option "Also on 'Position: Manually' Articulations").

Certain articulations can be automatically hidden in the score. This might make sense for bow marks, breath mark commas or certain shape articulations (e.g. brass fingering).
These can be selected in "Hide These Articulations in Score Only".
By default, only bow marks are selected.
The option "Reveal Accidentals on False Tied Notes" shows accidentals that were forgotten to add and only disappeared because of Finale's function to automatically hide accidentals if a note is tied.
This helps detecting wrong notes in playback or even wrong ties.
If the tie was correct, it also looked correct without the extra accidental. But if the accidental is revealed by the plugin, it will look wrong.
This option is more important if you work with playback. It is not recommended to use it, if you work without playback.

Image 2: Left: Original, Right: Hidden accidental revealed
It is recommended to let the plug-in remove all manual slur adjustments by selecting "Reset Manual Slur Adjustments". Otherwise slur optimizations may not work.
By default manual slur adjustments are removed, while manual curve adjustments are not because they are very often "hand-made" to illustrate a more complex behaviour.
To remove faulty manual note positions that were created accidentally, the Perfect Layout plugin has the option to do this automatically according to Finale's settings from Document Options. If the option "Automatic According to 'Manual Positioning' from Document Options" is selected, then .............

The option "Move Single Pitch Notes on One-Line Percussion Staves Onto Staff Line" is required for 1-line percussion staves where the notes are not centered on the staff line. This occurs from time to time in older documents or when imported through MusicXML.
This feature only becomes active when only one pitch ("Single pitch") is used throughout the staff. It will not do anything for example to two-note conga or bongo staves.
The option "Reset Left End Point Offset of Lines That Start on Measure Pos 0" is helpful for most custom lines as it is difficult to place them with a horizontal offset 0 on first try.
But there are, of course, scenarios where this option should better be switched off (especially in contemporary notation).

Image 3: Left: Original, Right: Start position set to horizontal offset 0.
"Clear Manual Vertical Lyrics Positioning" removes all manual adjustments. They appear especially in imported MusicXML files.

Image 4: Left: Original, Right: After vertical reset
"Force Tuplet Brackets on Ambiguous Tuplets" adds tuplet brackets on beamed notes when the tuplet doesn't start on the first note of the beamed group and thus is difficult to read.

Image 5: Left: Original, Right: Added Brackets

Another tuplet feature which can't be unselected is automatic secondary beam break insertion as in image 6:

Image 6: Left: Original, Right: Added secondary beam break

"Force Tuplet Brackets on Unsymmetrics Tuplets" adds tuplet brackets to unsymmetrics tuplets (i.e. if the duration of the notes is different from left to right than from right to left). In these cases it might be difficult to decipher the reference duration of the tuplet.

Image 7: Left: Original, Right: Added brackets only to unsymmetric tuplet to not mix it up with a 16th note tuplet

"Increase Tuplet Number If Max. Note Duration Is Shorter" changes the tuplet number for better readability if it doesn't match the note durations. I.e. six 16th notes with a "3" tuplet number would be transformed into a "6".

Image 8: Left: A five 8th note tuplet with 16th notes becomes a ten 16th notes tuplet

Note: In the Silver edition of the plug-in these three options are on the "Tuplets" tab.