Each NPC that is tracked into Tier 1 or Tier 2 will have individual goals. Such as get rich, become faction leader, avange family, revenge etc etc. This will get expanded into more like build settlement etc etc.
Currently there is not bounty system but this will be a feature for sure.
"or if a faction attacks your base due to your bad reputation, will they actually care to arrest you instead of leaving you unconscious"
This is tactical layer. As soon as those NPCs spawn Kenshi takes over, although I have implemented a way for de - virtualised NPCs to retain their waypoints from the sim into Kenshi. I currently haven't modified any files to alter NPC logic.
So short answer is a no on that one.