Righty-o, so, I played through the level 39 boss fight, and here are my thoughts:
Could use a couple of extra shakers in those unlockable compartments. I played on Hotshot, managed to hit him with every shaker in the room, and still wound up finishing him off with guided missiles and smarts.
The arena gives plenty of spots to hide, compartments to duck into to dodge the missile offspring etc... which is mostly good, but has the downside that it can be very frustrating to find the boss before your cloak or invuln wears off. If you're using the shakers, it's pretty safe to say you're probably not going to manage more than one hit on him for each cloak or invuln you get. We'll need to take that into account when we get around to deciding on the final number of those in the room.
The drone matcens introduce a lot of RNG when the boss winds up near the top of the room, because your Earthshaker bomblets will track them instead of the boss. Combine that with the limited number of shakers and that upper area can seriously screw up the fight. This could be mitigated by switching them back to spawning cloaked lifters the way they did in Xfing's original version, and removing a trigger or two so they spawn a little less frequently. This would also help mitigate the problem of hunting the boss down before your cloak runs out.
If you want a little more challenge from other bots in the room, I'd be curious to add Boarsheds into the spawn pool as well -- they'd give you more stuff to dodge but also allow you a steadier supply of smart missiles that could be used on the boss if you run out of shakers. I don't know if it would really work but it would be interesting to test.
Whether those matcens spawn melee bots or even just tougher bots, the player should certainly be allowed to have a helix and/or fusion cannon by that point in the mission so they have a quick way to clear out anything trying to body-check them on the way to those four vital compartments.
Wouldn't hurt to add a couple more mega missiles into the arena since even with a couple more shakers available we'll still be limiting the player's supply of effective firepower pretty severely. Especially true if the Boarshed thing doesn't work out
Megas might not be that effective unless you're cloaked, but that's still a strategic option. People like strategies and options.
And lastly, the boss fight is a very slow, deliberate, and patient affair-- which is great. However, we should keep this in mind when we're picking the level's midi track, 'cause if the song doesn't reflect that deliberate and patient hunting, it's probably going to get annoying for people. The best choice will probably not be a typical "bossfight" song.