The Guardian is probably too powerful for a player ship. In this mod it spawns a large number of derelict drones over time, has even more powerful stats than the Radiant, and has the same ship system.
I just personally not fan off things in games when NPCs have stuff what player can't have for some reasons, take for example first Half-Life and Half-Life 2, in first game player have access even for alien organic weapons, while in HL2 arsenal is both very scarce, and it has NPC only stuff, like Alyx SMG and emplacement Sniper Rifle in Episode 2 which player can't use despite they looks really cool.
So I liked ability to be capturable just for that reason, especially its looks strange for lore perspective, why one specific drone can't be captured at all, its looks logical for Omega drones, because they are something what no one saw before, while these Guardians appear both as keepers for Cryosleepers and appear in bounties, again as idea how make them not absurdly overpowered, you disable that drone spawning, make a bit toned down stats in player-captured version, and explain it in description like it is some battle damage which no one know how to repair.
And in late game you already capable of destroying pretty much, you already need to be strong enough to defeat it in first place, and enemy ships in vanilla not always recoverable even with story points.