The tol'vir probably made the overall shapes (pyramids etc.), nerubians gave it the more creepy look and then finally the Scourge added bones, magic, skulls to form the architecture we know.
I mean, it's not meant to make any sense. It is a retcon after all. We can see this all over the more recent lore. It's usually just less cut-and-dry.
I feel like at this point Blizzard is trying to gaslight people who played the earlier Warcraft games/versions of WoW.