The usecase is managing, updating, or copying tiles in a tilemap image.
Currently if you are using multiple layers in a tile set (for example underlying rocks, grass on top, decorative vines), and you want to copy/move a tile or set of tiles to re organize, or make a new variant, you have to select every, layer every time. It would be nice to select the layers you want to effect, then be able to do multiple Marque and transform actions in a row.
This could be a global option, per file setting, or a modifier key chord.