Reminds me of that event in FTL where you can encounter a version of the boss ship that is still under construction.
Speaking of boss ships, I really want to know its component health numbers. I feel like every encounter's goal is to smack its armor as hard as possible and follow up with explosive spam. I also don't know if the boss ships change strategy or activate new weapons or what in each phase. I'm going to ask the devs about that next time I see them.
FTL also had events with enemy anti-ship batteries (like attempting to fight the rebel fleet directly), though I believe the boss was never paired with them due to the sheer amount of time it takes to kill a boss even assuming the fight is completely one-sided. Here, one would have to take down the anti-ship guns before the boss for similar reasons.
As for this idea, 1-2 minutes for rearming is absurd. You can kill a boss in under a minute under its normal spam conditions. Same condition here, assuming you can deal with the other defenses. On the flip side, if it takes a while to break into the defenses, you now have a full-power boss to fight, and many of them. A more reasonable middle-ground is a boss missing some of its weapons (like the frontal heavy gun) and some of its health, but guarded by anti-ship guns (making it seem like a shipyard where the boss ships are constructed).
FTL's version was a boss ship that was down a few shield levels, had less than half the hp of the final boss, lacked one or two weapons (ion spammer was gone, I think), and lacked the ridiculous boss abilities (drone spam, laser spam, instantly regenerate 4 layer Zoltan shield). The defenses for it were the fact that you were flying in a rebel-controlled sector (shops very rare, benign beacons almost non-existant, combat encounters very common).
