Damon's prob my fave character, too, but I do think you might be reading into him a bit incorrectly... I don't think the Chapter 2 and 3 motivations contradict because even though Damon doesn't judge the MC for who they are (which meshes with his Ch. 2 attitude), he doesn't care for the MC more than he does the gigantic potential reward of turning them in. By this point, hasn't it only been a few days or weeks? It's Damon who states that turning the MC in would be enough to clear literally everyone on board's bounties, so... I actually think that fits very well with his tendency to have certain people's backs. We just aren't priority, quite yet.
And as for him not apologizing but then wanting to explain himself (? unfamiliar 'cause i haven't played the patched update yet), I still think that makes sense: Cal rejected the idea and Damon has no intention of making him reverse that decision. Everyone has to be on the same ship together and in some cases (*ahem* my MC's), Damon still might have to be your mentor. He def comes off to me as the type of person to want to air everything out at once, regardless of tact or timing, especially since I imagine 1) the others might give him crap for voicing that idea in the first place and 2) the MC is likely to get involved in more high stakes situation just by virtue of being on the ship, so Damon wouldn't want any unsaid bullshit to interfere with his ability to keep the others (and yea, prob even the MC) safe.
lol i am also the type of reader/player who deeply reads into interesting characters and Damon's captured my interest quite a lot. I enjoyed reading what you had to say about him, though. I think it'd be fair for the MC themself to be confused by these somewhat contradicting attitudes, though!