OK, so I tried the subtraction again after replacing one building that had a complicated patch for tops and bottoms with a very similar sized pure box, using the 4 point box command. I found another building with the same problem, corrected it the same way.
That got rid of all the annotation dots, and the difference kept failing.
Next step in trouble shooting was to check to see if you had a lot of coplanar faces. Like faces on subtractors in the exact same plane as on the stock. And there seems to be some of that too. By shrinking your bottom stock chunk from .750 to .745, the topography subtraction works. you could also nudge the topography down .005 or .002 or whatever. Doesn’t matter if it’s under .01, you’re not making an engine, nobody will notice.
Anyway, yeah, look for coplanar faces, ideally fudge the position of the subtractors a tiny bit to change that, and it ought to start working.
This is a bug that was worse in Rhino 5, when coplanar faces or colinear edges almost always caused a subtraction fail. Now it seems like (anecdotally, not sure) it takes a more perfect overlaps happening at the same time to get this problem.