Success! My bot now generates a viable navmesh, here is de_dust:
You'll notice some odd little islands here and there, that's just where I've not quite culled the geometry that is inside the map, but not actually reachable by the player, like on top of pillars and walls etc. It's not really a big deal for the moment since they're disconnect and therefore wouldn't form any part of a path anyway.
Now let's get the bots moving around