Not sure how the actual programming works, but it might be pretty easy to do. If the interior was designed properly you would just need a hole created in the terrain that would let you access the lower levels. Anything below the 1st or second floor could be enclosed and self contained.
What would be great though is if this could be used with a cave. You basically have the windows of the building open, the terrain would generate around in slightly into the building, and then a cave could connect to it at a lower level. Imagine just having the first floor peaking out of the side of hill, you go in, descend to the lower floors and find you can climb out of a window into a cavern.
I have a feeling at the moment the terrain generation occurs first, then later the monument system comes around and places things randomly in a nice spaced properly flat areas. I don't think it can alter the terrain once it is in monument placing mode. This will take a fair bit of reworking between the systems.