Sorry, modifying existing vanilla items and whatnot is really difficult. I can't think of a good way to do this without creating another item- though it's not nessisarily the worst option. If you just make a procedure that triggers on entity spawn, checks if the entity is an item entity, and then checks if the item entity is a waterbottle and replaces it with a modded water bottle, you'd be set. Might cause conflicts with brewing though.
Sorry, modifying existing vanilla items and whatnot is really difficult. I can't think of a good way to do this without creating another item- though it's not nessisarily the worst option. If you just make a procedure that triggers on entity spawn, checks if the entity is an item entity, and then checks if the item entity is a waterbottle and replaces it with a modded water bottle, you'd be set. Might cause conflicts with brewing though.