Just had a Basilisk win against the flagship, and I am really starting to see the glaring weaknesses that the boss has. Still though, that's kinda the whole point... Taking on a brute like that in his own game should be an insurmountable challenge. That's why you're supposed to use the force and send a blast down that one unprotected exhaust vent, and... No, wait, different thing...
Basilisk was really quite fun, because you get to see just what a change having a four-person boarding party is. Not once over the course of every event and every shop did I find a bomb weapon (there was a pegasus missile launcher at the start, but that was it), so I thought medbays would be a big issue... Then I discovered that when you have four elite mantises (or just two mantises and two rockmen as it was for a while) in a room together, they're capable of overpowering a crew to the point that the medbay will be full of recovering soldiers and the rest of the crew won't be able to pack in, so they just stand and die. Other times, the DPS is so great that they can't even make it out the door before they just fall dead to mantis phlegm.
But to point out how susceptible the boss is to boarders, when I was trying out the Nesasio first time around, I wound up winning thanks to my elite boarding team... This "elite boarding team" was comprised of an engi and a slug. Thanks to some truly sadistic RNG rolls earlier in the game, I'd lost not one but two actually decent boarding groups, and these were the only spare guys I had left. They were still enough on their own to overpower the weapon rooms, but taking on the main area required some tactics (also some bombs). In the end, they still managed to depopulate the ship and then sabotage the shields system, which meant... Well, it meant what it always means.
I also unlocked the stealth type B on that run, and hoooeee! That thing takes some hilarious amounts of luck to not crash and burn horribly.