Hi Mira, I've been running your mod for multiple playthroughs and I've been really enjoying these weapons, but I think I encountered a bug related to the new magic bounties from magiclib.
I was offered a hegemony bounty via the unsanctioned bounty board in the bar and it was about hegemony testings superweapons, in the previews, the onslaught flagship of the fleet seemed like it had 3 MX Gauss Cannons equipped, but when I actually got to the fight the superweapons were not present, the onslaught had empty weapon mounts where the MX cannons would have been. I am unsure if this is an issue with the superweapons being unable to be used by the AI factions or is it an issue with magic bounties.
(also I'm assuming this is what you meant by being able to obtain superweapons via missions or methods alternate to just exploration if the bounties work and there's enough of them then I'm 100% down with getting these weapons off of tough fights)
Regardless I still really enjoy this mod and I wish you happy holidays!