My headcanon is that in public / guest quarters the toilet stalls contain miniature holodeck emitters so that they can instantly change to accommodate the customs / biology of any species. Even assuming that, say, Klingons excrete waste from the same places that humans do, they might prefer to do so while dangling from a bar in the ceiling or something else torturous like that, and find the use of a regular sitting toilet unclean or dishonorable.