I used Xenochemistry on a potion and turned it into an Aqua Regia. I tried to stack it with my existing Aqua Regia, but it wouldn't work - they just swapped with each other. I'll try it again later with a different potion and see if it's stackable or not.
I had similar issues. It wasn't consistent though (as far as I noticed). Sometimes potions (of various types) would be made that wouldn't stack, sometimes not. Sometimes I'd come back to the game and they'd stack again...
