Hey there,
kartoFlane! I just had my first run with your ship (which, incidentally, was also my first run with custom ship ever) and I liked it very much. Really nicely done! I especially loved the RP element of being ships' AI instead of regular Captain. Not to mention challenging, but interesting gameplay with this infernal beam ( infernal unless you're attacking pesky slugs ships with their Slug Gel, that is - but it's still fun to smash them

).
As you may guess, I was playing it with Captain's Edition, which as I've noticed is even recommended by you for this ship. Thus, I've come with very simple technical change, that would make playing it with CE even more fun. As you probably know, CE introduced faction differentiation, which, for some ships, focuses around piracy. Now, your ship replaces Engi A, which makes it quite probable that our crew will deny order to attack civilians (even if we don't have crew, actually!), or get upset, at best.
Now, for some reasons, Auto Cruiser with his little sinister AI seems to me like a thing that wouldn't have problems with piracy or betraying enemies that have surrendered (Rebel AI ships in CE break surrender truces too, pretty often). So, I would suggest that your ship could replace Slug A/B instead of Engi's. AFAIK, it would also require to give player and augment that is tagged as characterizing slugs in CE (dummy Stolen Tech could be used for that purpose I think - players could still sell it, or keep if interested in pirating).
I would make ship over-powered - especially, that forcing surrenders in CE require dropping enemy's hull levels to very low values *without* killing its crew beforehand, which is extremely hard in Auto Cruiser - but would make it definitely more sinister

The only thing that was a letdown during playing this, is that my re-purposed rebel AI was unlikely sensible to Civilian's suffering

Cheers,
/Estel