When I place a purified water source block down and in a pool and then try to fill bottles from it I get regular water bottles. I would expect that it would return purified water bottles instead.
Build 1.12.2-3.1.0.124

It could consume the purified water source, which would prevent that exploit and make more sense.
Also, you can't fill canteens from these sources either. The same idea could work for that, it would consume the source block.

That could be an option but it does open up a whole lot of work that needs to be done to be compatible with other mods' fluid mechanics. How much should a bottle use? How about a bucket? I know some mods equate the two and others don't.

Based on Cauldron interactions, one bottle is about 1/3 of a bucket. Filling up Purified Water Bottle from a Purified Water source block could take it all, resulting in a "loss", but it's easier than adding 1/3 source block and 2/3 source block, which would look weird.

This probably isn't a bug... if that worked that then you'd have infinite purified water for no cost and that's entirely against the spirit of the mod.