I don't see the issue here. The Bolians were concerned about early 21st century human plumbing, not modern, super-advanced plumbing on a top-of-the-line starship (no doubt inspired by early Vulcan interest in starship development, and further made cleaner by the thousands of civilizations - including Bolians - who had developed the greatest plumbing imaginable).
The first quote in this thread shows that functioning lavatories are high-energy using systems. Probably self-cleaning in an order of magnitude even greater than that of a holodeck.
In my judgment, using a fully-functional lavatory after a Bolian has exited involves no risk. I may be concerned, however, if there are multiple toilets and a Bolian walks in with me.