I agree that there should be a way to toggle in buildings in sandbox in order to make them not count against you. However the smell/sound of many of the buildings is understandably proximity based.
Personally, I build 3-5 exhibits that all surround a hub of staff buildings. Makes for easy staff groupings and very short travel time between buildings and exhibits. If you go the underground option you can still place the buildings under paths, but they need to be deep enough. The building have a spherical hitbox, not a cylindrical one. So, if you are far enough above or below the path then guests will not notice. If you wanted to have a floating staff city, or a cave network, then you could as long as it was far enough up or down. The main drawback is that you really increase travel times with having to go all the way up or down stairs. I know Disney has a network like this, but it is mainly for quick traversal across the park and maintenance, both of which are unnecessary here. Also, I THINK that power/water buildings also have spherical influences, so this limits how far they can reach.