You could just make it so that floor tiles spawn on top of buildings (Basically when you generate the z+1 level, make it so for every coordinate that had a building tile underneath it, spawn a floor, then add the special stuff like church towers). No need for level design.
Perhaps, but don't see why would anyone go there if they are not designed with some particular features to at least make them different from one another. I was hoping Acidia would eventually design top floors for his new buildings, like office towers, hotels and apartment buildings.
By the way, what does it matter what the DDA guys do? Right now, the only way I can inteprete your comment is if a) You're in some kind of futile "my-****-is-bigger-than-yours" fight with them, or b) you're waiting so you can copy their code and save the hassle of making z-levels yourself.
I don't believe the feature fits in the game, I think even with perfect execution it would make it worse, slow and tedious. I'm open to the idea though, but I don't want to invest my time into experimenting with it, easier will be to learn from their mistakes.
Anyway, what exactly do you have in mind for mission and scoreboard?
Missions would concentrate gameplay on visiting special areas and killing special monsters. Quicker time to complete a mission would give better score.