I think not too many of the false exits we find in the games were actually collapsed from above, but simply misleading tunnels that don't make it to the surface.
I do recall at least one of the false exits in A1 being described as failed mining attempt to dig up and out. Avernum is likely extremely deep beneath the earth and any exits would require great upward distances. The caves west of Remote are miles long and I seem to recall they sloped upwards almost all the way north.
I would strongly suspect all the exits that were used by the Dragons and GIFTs weren't usable by humans. They could very well be giant vertical shafts up, as Dragons can fly and GIFTs can walk up walls. Their mouths could be on the roof of the larger caves, miles above, totally inaccessible.
My confusion over the entering and exiting of Avernum relates largely to the number of what I assume are ancient human crypts found in the series, as well as the various Liches of great age who speak the same language as us without any accents. I always assumed they weren't Vahnatai as they have their own distinctive undead, and our party specifically notes that one Vahnatai shade in A1 as being clearly alien from ourselves.
Though Jeff could use a generic model for all skeletons/zombies wouldn't he at least describe them as being clearly not human undead (wouldn't Slith skeletons/zombies still have tails?)
Could there have been humans living in Avernum long before the First Expedition? Possibly wiped out by the Sliths when they emerged from the lower caves?
There's the Vampire near Formello, Drath, and there was clearly more undead within the Spiral Crypt than just the party of the First Expedition who met their grisly end there. Even after killing their ghosts, and purging the area they died in in A2 the undead were still strong there. I get the sense the evil there was very very old.
The one in A5 is clearly a human crypt as we see the human ghosts, and is described as being incredibly old. Plus its location is in the frontier which was new to the Avernites in A5.