I was trying to make new recipes for the Magic Bees flowers, and it seems that anything other than petals, powder, and runes will not be accepted by the apothecary (I was trying to include a bee in the recipe). Also, the original (bugged) recipes have Fire as a placeholder, so I thought I'd try that before attempting a fix, and Fire is also not accepted in item form (my pack has an obscure way to get fire items).

A fire-like item is the default in recipes if an item isn't registered. What you're seeing is what used to be the Mana Petal.

I know, but I figured, since my pack actually has a way to obtain fire (via disarming Fire Elementals from Ars Magica) I'd try the recipes anyway before fixing them, but the Apothecary doesn't accept fire.

it's not a real item, of course. fire's just used so it doesn't crash.

I then tried to make the new recipe include a bee, since it's a Magic Bees flower, but it wouldn't accept that either. It seems to only accept a limited list of items, and rejects everything else. Is there a way to add more items to this list?

No, as it's not a list: the item must implement IFlowerComponent. An addon could do it to their own item, but Forestry would have to manually declare their item as an IFlowerComponent.

Alright, makes sense.