...hm.
Maybe the final boss is... An alchemist? A magician?
Wait! I just realized it! This is some experiment of Patchouli's or Alice's(or both) that has gone wrong, and the reason that Sakuya didn't know is because not even the magician in question knew at first, if she realizes that this is happening at all...
On another note, since we are talking about possessed objects and what not, should one expect Medicine Melancholy to appear in this game? I would surmise her to be a possible midboss, either of Stage 4 or Extra.