Well, the toilet thing can be handwaved given Eorzea is at an uneven tech level and socially at least, is somewhat equivelant to the early 'modern' (read: 1700s+) era (despite some advancement), meaning most people would not have anything remotely advanced in their homes as a flush toilet, instead they would just use for their ablutions something basic like a chamberpot under their bed. In fact, a low level FATE in Southern Thanalan called 'Downwind' strongly suggests most toilets in Eorzea are latrines that are little more than a hole in the ground outside that collects the waste, which naturally attracts unwanted pests and vermin.

So really the lack of toilets is easily explained as something somewhat too technological for the setting.