Finale is in most cases able to resolve conflicts between objects in different layers, but only if they are at the same rhythmical position. Collisions of elements in different layers and at different rhythmical positions, like augmentation dots, accidentals, [long] lyric syllables on [short] melismas, etc. are ignored entirely by Finale, requiring the user to resort to manual tweaking, most of which gets undone if the music gets respaced (regardless of the Manual Position setting in Document Options). Here's an example with augmentation dots:
Here's an example with accidentals:
These basic issues really need to be addressed. FWIW, version 1.1 of Dorico, which is only 6 months old, is able to space these examples perfectly without any tweaking. If anyone's interested, I can post these examples done in Dorico.