Collision layers can be used for only letting certain actors interact with the tilemap, e.g. the player can collide with the tilemap but not the enemies.
I guess collision mask could be used if you want to put collision logic on the tilemap itself.
Is cell transposed can be used if you want to do something if a cell is altered in any way?
The update bitmask stuff can be used if you want to modify bitmasks in code instead of through the editor.
Update dirty quadrants is for if you just modified the cells of the tilemap and you want collision and navigation to also be updated right away.