Kyronix, can you expand upon what data is not set in the objects? Is this data that should impact gameplay? Why not set default values for those which the barrel painting lacks so that they are compatible with the player crafted? Haven't we been down this road multiple times before...?
Any potion that comes out of the alchemy crafting has a "power" value associated with it, this is important for the older potions (heal, cure, etc) but has no effect on newer potions. To fix it we would do as you stated, setting an arbitrary default value so they stack...just a matter of making sure that arbitrary value that is applied to the crafted version is the same as the ones you get from non-crafting sources...which it may or may not always be.