Ok. So maybe 8" to 10" throughout the whole cage might be better and see how that goes. Would the nice apartment house still work then? The main idea of deep bedding is so they can dig tunnels but that's only really possible if the substrate is deep in the entire cage kind of. And he may not be doing it anyway if he likes his subterranean hide. The main thing about having it all the same level (still with his nice items you have) is it could be easier to get him into a routine for getting him out and taming. You may be right that he feels a bit exposed in the lower/more open area.
When I get a minute, I'll go back and look at the cage set up and see if I can make some suggestions
While still using the same nice items. It would be nice if he would come out early evening for food and at that time you can tempt him into a tube and have him out for some taming in a playpen.