I think q!cellbit’s treatment of q!pac starting with that first message during the fed worker murders stems from the fear that q!pac will inevitably betray and abandon him like he did on that island after their escape from prison. That fear causing him to want to keep control over q!pac by weaponizing q!pac’s fear of him. Which then conflicts with him also wanting q!pac to be happy and safe causing his self-esteem to continually sink.
Its one part of the continual cycle of q!cellbit falling back onto the violent and manipulative tactics he learned and had to use to survive during his time in the hunger games, the war, and prison when he or someone he cares about is threatened, feeling shame about the fact that he does so but justifying it by saying that it’s because thats just the way he is instead of acknowledging that he is not his trauma responses.
By this explanation, the reason q!cellbit left the first message during the murder of the federation workers would be because of the first part of the explanation (acting because of the fear that q!pac will betray him again) after noticing that q!pac’s fear of him had resurfaced. I would also argue that his fear of betrayal and abandonment was exacerbated by the disappearance of the eggs and the 2/5 of the favela five being missing in the nether or in a coma (i’m not counting felps as missing because felps)
The same can be said for a majority of their interactions during purgatory 1 (&2 depending on if cc!pac has purgatory 2 be canon for his character).
However this explanation also accounts for the few interactions in which q!cellbit is not hostile to q!pac, Most notably their short talk after the warzone event on day 13 of purgatory.
In this talk q!cellbit says that q!pac did well today before walking off. This is important because during the event q!pac got a kill (or maybe 2? I need to double check) on q!cellbit.
With that knowlege, it would be expected for q!cellbit to react with anger and violence at loosing some of his control over q!pac but he doesn’t because at the end of the day he cares more about q!pac then he does himself. He wants q!pac to fight back, he wants q!pac to not fear him both because if q!pac isnt afraid of him he has less reason to betray/abandon him and because he knows his actions cause q!pac distress and are wrong (q!cellbit saying that the posters q!pac put up around chume labs are valid is a good example of this)
To go more into theory territory, I can see q!cellbit wanting q!pac to be the one to put him out of his misery and be the hero of the story.
During the happy pills arc, q!cellbit consistently acknowledged q!pac’s strengths and intelligence. He’s under no false perception that q!pac is weak of mind or body but he also knows that q!pac’s fear of him when coupled with his low self-esteem leads him to not use his strengths.
I think that in q!cellbit’s mind if q!pac can overcome that fear and self-doubt than there is no reason that q!pac can’t stop his vicious cycle of violence and self-destruction.