Version Information

Forge version: 1.15.2-31.1.18
Botania version: r1.11-379 & r1.11-378

Further Information

Steps to reproduce:
https://www.youtube.com/watch?v=9MlUY10--N4

If I move the apothecary one block down, it works but reduces compactness.

What I expected to happen:
open crate to accept the filled bucket and refill the apothecary

What happened instead:
filled water bucket stays in the hopper, open crate doesn't accept it. It looks like there has to be at least 1 full block between the apothecary and the open crate.

basically the problem is it checks "is there a block here" instead of "would an item entity fit here"

Fixed the problem described above (the open crate will now check if the item will fit where it spawns it instead of just checking for a collision box anywhere in the blockspace

However, that wouldn't resolve your original issue, because the apothecary's collision box extends above its blockspace. Unfortunately, not much can be done about that.

For super compactness you probably want a dropper facing sideways into the apothecary, since the apothecary does collision checks for items on all sides of itself, not just the top.