Currently compiled and testing out the 1.12 version. Am on this version:
7ff0fd2

Made an alchemy catalyst pool, threw my tablet on to it to fuel it, and it just ate my tablet.
Tried to create melon seeds from beetroot seeds, also got nothing back.

Seems to just void items thrown into it regardless of whether a valid transmutation is available. Possibly the reason behind #2258.

Did some investigation into this and figured out the issue. The Mini Flower recipes are being registered as having both an input and output of Air blocks, and this is interfering with all other alchemy recipes.

The ofType method in ItemBlockSpecialFlower calls new ItemStack(ModBlocks.specialFlower). This eventually calls getItemFromBlock(botania:specialflower).

The problem, however, is that when registering the mini flowers (and probably when using any Botania block as an ingredient in mana pool crafting if I understand the issue correctly), the recipe is being registered before the Item.BLOCK_TO_ITEM map is populated with Botania's entries, resulting in ofType returning Air blocks instead of the correct ingredients.

I was able to fix this by moving the call of initTileEntities() from the end of ModBlocks.registerBlocks to the end of ModBlocks.registerItemBlocks. I'm not sure if there is a better place to put this method or if this change could have other, breaking impacts, so I won't make a PR for it, but it seems that the issue is entirely fixed by not calling initTileEntities until registerItemBlocks has been called.

that seems like a reasonable fix, you can make a PR for it