I think I'm going to go with the usual interpretation that cities in the lore are physically bigger than portrayed in game, so the Silent City would probably have more buildings and rooms. It would give us a bit more freedom with using it. 

Also, you could have Sabine take part in one or more of the research projects, if you wanted. I think Meesei would have been trying to help with them however she could. She knows very little about the Dwemer, but anything relating to enchanting she would have liked to be involved in. Ahnasha would be doing her own, private necromancy research away from the Silent City, as well as training with the Breton woman whose name currently escapes me. All of those skeletons probably would have been useful to her.