I'd imagine under normal circumstances a vampire lord of Alucard's calibre would be in control to the extent of being able to decide how much somebody from within could manifest itself. I doubt he would allow Schrödinger too much luxury in that respect (never as much as Seras is giving Bernadotte). So, I think he can separate the special powers (and knowledge) of those he absorbs from their personality, although I still think his own personality will be affected and changed by the traces of those he ingests. Thus, he gained Schrödinger's troublesome power and disappeared. But you are right that it must have required him to kill all the extra souls within himself to be in a position to get in control of Schrödinger's power. If it's a power that requires the mind to be of one opinion whether to exist or not, then having multiple minds pondering it would never be any good.

Who knows, but it's not relevant anymore with the story over.