I have no clue how you managed, but I can't get this vmf to stop leaking, even with cordon. Okay wait, turned on all user visgroups and now it will stop leaking with cordon (that doesn't touch the edges of the hammer grid). I didn't know user visgroups could do that, but I don't use them very often.
Also, when I toggled on cordon you had it sized to map extents, so I have a feeling you were compiling with cordon from the beginning and that was what was creating the unbound volume areas. Just going off the fact that you have a few holes in that box area leads me to believe you were compiling with cordon. I should note that for all the compiles I tried I didn't get any of the unbounded error messages. So either you've changed something about the file before uploading it or it was compiling with the cordon at map extents causing the errors.
Beyond that problem, I think you shouldn't be mapping on the 1u grid size because that's just bad practice. And for the 16000u hole, do what you will, but I think it's pretty ridiculous distance. Also, what's with the grouping on the doomsday_event fortune teller rip? It doesn't respond to ungroup and every piece of the structure has one of those radial fade boundaries.