Finally finished the map with 13.13 hours of playtime (100% kills, items, and secrets, in one go, without saving! Although with a few practice saves and noclip/summon to practice bossfight at one point.) and I have a few more comments.
The large underground caverns that you need the yellow key to access feel a bit confusing and empty, especially towards the end (that last room with tons of health and armor bonuses feels like it could've had more in it,) and it's very easy to miss a few enemies in all the similar-looking rooms and go looking for them for 10+ minutes. Also, the BFG secret is pretty cryptic. I had to look in GZDoom Builder to figure out how to get that one, and even then it took me a bit of time (mostly because I'm unfamiliar with GZDoom Builder, but still!) I thought I had checked that area already but apparently I needed to use a projectile which on most weapon-activated switches is the thing that doesn't work.
However, these are my only gripes with the map. The underground caverns really aren't that bad, just confusing at times and kind of empty. They still look great and mostly play well too, really the only weak part of the map in my opinion. The ending fight is enjoyable as well, feeling very fair and challenging (it might be a good idea to place some invisible walls or something out there though as I had a few instances where a caco flew stupidly far out and I had to wait almost a minute for him to get back in range.)
I also liked most of the secret placements, as they made sense and followed a pattern that could be figured out without too much trouble, although the rewards for a few of them were a bit underwhelming (looking at you, medikits.) Not sure what you meant by obtuse progression, as it seemed pretty good to me. You get the weapons in order of power and pretty spread out as well. It was very easy to figure out where to go, and also to remember where various key doors/switches were, as they were marked well.
As I mentioned before, the map looks beautiful. Hellish and unsettling all throughout, albeit in slightly different ways. Really liked when there were windows looking into detailed areas that you couldn't actually get to but were just there for decoration, it nicely added to the experience in my opinion.
Once again, great map overall! Really looking forward to seeing what you do next.