Persistent Enemy sounds like a feature that would work better to either stay modular, or have some kind of in mod function to be turned off because it pretty much kneecaps anyone who want to min/max the slaves they keep around (because of the low max slave capacity unless you cheat) while also role play as a pseudo good karma character.
With how base game's character progression goes, a slave's stats get their potential Maxed out around level 5 or so if I remember correctly, and what makes a Randomly generated slave flat out better than other by a fairly significant margin due to low soft level cap is to either have higher beauty rating (I usually only keep those that's at least at Cute rank), and have one of the four traits with a flat +2 stats bonus to one of the four prime stats. That's not even counting the species a randomly generated NPC belong to and try to grind one of the rarer race.
Granted, I can keep executing the random bandit till I get a new random one with both high beauty AND one of the four best traits. But I generally like to go for a non-lethal playthrough, so that option is kind of kneecapped for me.
Couple of ideas I have is to mitigate this is once again, keep the persistent enemy a modular mod that can work alongside with the big overhaul Expansion, have a function to turn it off in game within the mod, add a new option where player can exile the bandit rather than execute (essentially the same but for those who want to roleplay nonlethal), increase the softcap of every race larger so the +2 stats no longer matter a lot therefore make the four traits less OP overall (would also solve the problem with slime race can't be modded in laboratory problem), or rework the rebellion effect to expire faster either by default or add some late game upgrade to make it go away much quicker so fullfilling one of the slave guild request (particularly the 'good karma' one like bodyguard and merchant helper for those who want to role play a semi-good karma slave owner) so we can turn over the less desirable slave and make a profit much quicker.