Heh, it was so long ago I don't remember everything. Also I was only a regular Level Designer at time doing my own thing while everyone else did their individual thing. The PODs for example had 3 different interior looks because there was no Environmental Art Director. My 2nd iteration was making them look like the Nostromo. The Lobby at the bridge connection points was another style that Courtney did I believe. There was yet another version for some side rooms Dan Thibs did.
At the time in-game maps weren't really a thing as well as level flowing back-and-forth. I did my best to add Map panels on each floor and icons above each door frame to suggest what was further down. I'm pretty sure you can still put all the levels together into one mega level map to have everything connected with no funny overlapping rooms or hallways.
In regards to Harrison, I don't remember the story elements. There was a story crew who came in to all the levels to wire up the cutscenes. As with typical game development some things are cut for timing while others are cut because it didn't look right. This was probably the case with the cut models. Good ideas, but there was never enough time to make them good or give them exciting encounters.
Random related bit to game dev -- on the Turok game I worked on, a huge character was cut in the last year of production. You used to have a girl companion (inspired by Newt!) who followed you around in the jungles.
The file format issue was probably another typical "early days" problem with every studio trying to create their own engine, and therefore their own tech. Which meant there was little commerical support for it outside of "it works good enough" internally.
I think have a version of Maya 4.0 which featured a way to convert AvP Talon Engine levels to NOLFs Jupiter Engine. I remember the one thing they didn't get right was instance scaling of some textures... so some would import either too big or too small to their original use. Once in Maya though, you could in theory export levels to any format (as raw polys and no longer BSP).
It'd be fun to do another level! All my time is spent learning new tech for my current projects so I haven't had time. Like I said before though, it'd be awesome if someone like Fox or Sega would remaster AvP2. Rebalance some known issue and give it some modern Console perks.
