I think the reason the reactor core version is preferred is because it's just a lot more "epic" a death for the big bad Emperor, even if it makes no sense at all. I think TV Tropes calls it the "Rule of Cool", instead of the Emperor of the galaxy being killed by Darth Rorshach Vader throwing him down a lift shaft and him exploding for some reason at the end, being thrown into the reactor core of his own giant battlestation is a much more "dignified" death.

Still, if you can't reconcile the two things coming together (almost nothing in SW makes sense really, it's science fantasy rather than sci-fi really), I guess a new matte and maybe a new reveal of the tower is in order.

P.S. For some reason, as a kid I never actually clicked that the Emperor's throne room was in a tower above the surface of the Death Star, I though it was just on the surface, so I never thought it didn't make sense that he fell to the reactor core (massive distance covered in too fast a time aside, my kid brain didn't consider that).