I just fought the final boss on CEi. Maybe it was just my loadout, but it was indeed much harder. Which is a good thing.

I have a couple suggestions though.
For CEi: I think the Defense Drone 3 should be limited to the 2nd stage. Only because the 2nd phase is still the "drone phase" and the 3rd stage I've always thought was the more "tank phase." It seemed like at least 3/4 of the shots I got off missed so I could barely hit the boss anyway and the little damage I did was repaired by the Hull Repair Drone when the Zoltan Shield recharged. I think if you really want it to have a Defense Drone perhaps you should give the Boss a slightly less strong defense drone on this phase since it is hard enough already and it keeps the drone phase a little more distinct from the third phase. If you want to keep up the difficulty maybe just increase the engine power even more. I don't remember if it already has max power.
The oxygen being instantly depleted on this stage is fine for CEi. It prevents you from boarding at all. Maybe try giving the Boss a lvl 4 teleporter though because that should be instant or really fast cooldown. That or slightly increase the number of boarders because the boss seems to suffocate its own crew too fast. And for both CEi and regular CE I think you could add some text to explain why some of the crew still dies. You could explain that there is an oxygen leak and that is why they are trying to get off the ship. It you could say a few brave soles stay behind to manually initiate the FailSafe, which is the Advanced AI.
Also, I don't think it would be too bad to give the Boss some drones on the 1st phase as well and connect the weapon rooms on the 1st & 2nd stages. And maybe decrease the charge time of the artillery. On CEi the artillery still seemed to come very slow so the 1st stage does not seem to gaining difficulty to keep up with the CEi curve. The charge time is fine on regular CE though.
For Regular CE: I think the Drone Uplink Jammer should still work on the 3rd stage drone control. Or maybe the text should at least explain that the AI is hack proof because I was surprised when my Drone Uplink Jammer did nothing, until I looked at the code and saw that all effects on drone control get cleared.
Perhaps it may not be too bad of an idea to make an encased drone control system on the third stage. The drones would still spawn somewhere, but then of course they wouldn't be able to heal which could be an issue
I don't think the AP drone that spawns on the third stage is necessary because you can't really board the ship anyway. Except with AI crew and even then whatever damage they could do would be stopped by the swarm of Ststem Repair Drones. Unless you really swarm the ship with AI. If you want, maybe you could give the Boss a 2nd system repair drone instead.
And last something that's not too big of an issue, but could potentially be an issue. If you kill all the crew on the 1st or 2nd phases the AU Boarding event can happen more than once.

This could probably be resolved by changing that event to an eventList which then calls two+ different events. One could be %99+ percent probable and unique, the other could be non-unique and not cause a boarding to happen a 2nd time. Yes this works, I've tested it. Don't have to do that though. It's your mod.
P.S. One more thing that's been bugging me for a while. Us the Boss Ion supposed to fire 4 shots?

I never really understood the point of that. 3 shots can already take out 2 shields if they all hit and the weapon only has 3 barrels. It is the only Boss weapon that shoots more than 3 projectiles. Do you think maybe you could change that back...
Also, glad to hear that the Infinite Loot script is working. Another use for that would be to create more variation of ENEMY weapons in main CE. They could all be changed slightly from the player variants slightly and that could be used even in the normal Captain's Edition.