Why don't I have a custom title by now?!
ZDoom can have "real" 3D floors, without any teleport trick. Several are prominently displayed in ZDCMP2.
-What are the limits of 3D floors, for example, in ZDoom? Can they be recreated without using silent teleporters? Are real floor over floor possible in ZDoom or EDGE? For example, if I want to recreate a real 10-floor building without teleporters, can it be done?
The only limitation is that they can only have flat surfaces -- no sloped 3D floors in ZDoom. GZDoom, however, allows sloped 3D floors (but they're a bother to set up).
One never knows what the future holds, but nope. It'd require a dramatic shift in design goals.
-Will PrBoom+ be able to play ZDoom or Legacy demos in, say, 10 years? Can it be implemented? Is it difficult, extremely difficult, or impossible?
It can be implemented (anything's possible after all) and the level of difficulty would mostly depend on how much of PrBoom+'s current goals you are willing to sacrifice.
Technically, yes, but it would be a real nightmare to code and maintain.
-Is it possible, for example, to create some sort of "Universal Source Port" that can recreate most, if not all, the features present in the more advanced source ports? For example, a combination of ZDoom and Legacy, or PrBoom+ and 3DGE?
No. ZDoom as it is now presumably supports all the vintage games it is ever going to support. Only possible additions would be some console ports, e.g. the dormant Doom64 branch.
OK, so it's possible to make them look like HL or Quake, but can they be made to act like them? For example, if I understand correctly, the first versions of ZDoom didn't have Hexen support. Now they have it. Will future versions of ZDoom be able to support "Quake clones"?
Chex Quest, Hacx, Heretic, Hexen, and Strife all stayed remarkably close to the original Doom engine. Adding support for non-Doom engine games (Build, Quake, whatever) would be too much work. There's a lot of little tiny details that would hinder extending the port towards other game engines, going from needlessly redundant systems to incompatible underlying architecture.