Actually I would prefer if it worked from anywhere in your inventory, but at the very least your offhand? becuase lets say im mining out a large area and dont want stone variants (andesite/diorite/granite)... Uh, they can only be mined with a pick. Am I supposed to mine them from a distance and then tediously switch to the bottle before I pick them up?

The point being, if this is somehow intentional behavior, it is extremely impractical to only work in your mainhand

It will work in any hotbar slot. Next version will fix it for the offhand.