The True Ending just makes me think. Viola on Ellen's witch body dies because Ellen's roses were killed by the cute little bottle. The description of the cute little bottle does say it will kill the witch's flowers, and one of The Witch's House secret books do say that the witch dies when her roses dies, hinting that she and the roses are one.
Though in both endings, after the roses die, Ellen still is able to go out of her house and after Viola (Or with her in the other end). And then when Viola's dad shoots Viola in Ellen's body, it's later seen that her body vanished just after the demon cat comes. It's mostly said that Viola does die in the end, but what if the demon was lying all along? What if the cute little bottle actually doesn't kill the witch? After all, why would he want to get rid of his feeder? It might just be Viola's soul inside a torn-apart witch's body serving a demon cat. If Ellen was possessed by the demon, then what would stop the demon from possessing Viola's soul.
In fact, could that be why Viola went mad at Ellen when she switched bodies with her? The entirety of the game might even be a possessed Viola wanting to kill Ellen. And why would Viola even let Ellen die while she still in her body? Wouldn't she rather catch her alive to get her body back? And what was Viola in Ellen's body even thinking off in the first place? If she doesn't know the spell on how to take her body back, then why would she kill Ellen?
Oh and I've just thought, shouldn't she know the body trading spell in the first place? Ellen's memories are in her body so why can't Viola take advantage of that? Maybe she's at loss at power? Or maybe something's stopping her from thinking about it, blocking the memory from being remembered. It's one more meal for the demon after all right?