The recipe to craft white chocolate bottles only empties the milk bottle rather than consuming it, creating an extra bottle with white chocolate in it.

Tested with MC 1.18.1, Fabric API 0.44.0+1.18, DawnAPI 3.2.0 and Culinaire 2.3.3 versions; reproduced in both creative and survival.

The recipe to craft white chocolate bottles only empties the milk bottle rather than consuming it, creating an extra bottle with white chocolate in it.

Tested with MC 1.18.1, Fabric API 0.44.0+1.18, DawnAPI 3.2.0 and Culinaire 2.3.3 versions; reproduced in both creative and survival.

I noticed this happening to me, took me until i realized I had 27 glass bottles instead of the 6 i originally crafted until i noticed...

I've been able to reproduce this myself. It's caused by recipe remainders, so I think I should just disable it? But that might also consume the entire bottle when crafting chocolate bars, so that's a bit of a problem.

I noticed that milk chocolate bottles also have this issue, for the same reason as white chocolate I'd imagine; dark chocolate works fine, so I think milk bottles are a possible cause of this issue.

One solution to this could be to make milk bottles have no recipe remainder, though that would cause problems should you want to make recipes that require milk, but not the bottle specifically. e.g original minecraft cake with three milk bottles instead of buckets.

The problem is that remainder is global to the item (usage and recipes), it's not part of the recipe itself. (at least, that's how vanilla does it, not sure if fabric breaks it up)

Item recipe remainders are defined in the Java code per item.
Item recipes are defined in the JSON files, in the datapack..
And the datapack is managed by the Java code

I am not very knowledgeable on the inner workings of the game, so I can absolutely be wrong about this:
Based on the fabric docs for items, recipe remainders are an aspect of the item itself like you said, but usage (eating, pouring into cauldrons, etc) I think is a separate thing.

Why I think this is because I was prototyping another solution, using mushroom stew as a placeholder for the chocolate bottles; when I crafted the chocolate bars with it the entire bowl, not just the stew, was consumed. Eating the stew, however, returned the bowl like expected.

Fabric docs I mentioned: https://fabricmc.net/wiki/tutorial:items_docs