Would it be possible to have an option on potions (and other consumables) so that when they are used they can be converted into another item...
Use health potion
Get healed by the potion
Health potion is removed from inventory and replaced with an empty bottle
You can do this already.
Add a potion (going to assume it's a drinkable potion)
Go over to Drink Events
Add the "Items: Clone and Move to Character" event. Set the first value to whatever item you want (a bottle in this case), set the second value to #user.
I do have a legitimate Bottles update planned for v5 that does stuff like this automatically (and also lets you dip empty bottles into specific types of mines), but you can use the events system until I install that.