even when all parties are acting in good faith, they know that they wont be able to reconcile about certain disagreements, and it may seem to make sense, from some perspectives, to try to just impose their own way, in those disputed regions.

Aumann's agreement theorem which is discussed in the paper 'Are Disagreements Honest?' by Hanson and Cowen suggests that perfectly rational agents (updating via Bayes theorem) should not disagree in this fashion, even if their life experiences were different, provided that their opinions on all topics are common knowledge and they have common priors.  This is often framed as saying that such agents cannot 'agree to disagree'. 

I'm a bit hazy on the details, but broadly, two agents with common priors but different evidence (ie. different life experiences or expertise) can share their knowledge and mutually update based on their different knowledge, eventually converging on an agreed probability distribution.

Of course, humans are not perfectly rational so this rarely happens (this is discussed in the Hanson/Cowen paper). There are some results which seems to suggest you can relax some assumptions of Aumann's theorem to have more realistic assumptions and still get similar results. Scott Aaronson showed that Aumann's theorem holds (to a high degree) even when the agreement of agents over priors isn't perfect and the agents can exchange only limited amounts of information. 

Maybe the agents who are alive in the future will not be perfectly rational, but I guess we can hope that they might be rational enough to converge close enough to agreement that they don't fight on important issues.

I have thought about similar things, with just humans as the subject. I'm hoping that the overlap is great enough that some of these ideas may be useful.

Firstly, what is meant by conflict? Hostility? more intelligent agents seem to fight less, as the scope which they consider increases. Stupid people have a very small scope, which might even be limited to themselves and the moment in question. Smarter people start thinking about the future, and the environment they're in (as an extension of themselves). Smarter people still seem to dislike tribalism and other conflict between small groups, their scope is larger, often being a superset of at least both groups, which leads to the belief that conflict between these groups is mistaken and only of negative utility. (but perhaps any agent will wish to increase the coherence inside the scope of whatever system they wish to improve)

Secondly, by thinking about games, I have come to the idea of "sportsmanship", which is essentially good-faith conflict. You could say it's competition with mutual benefit. Perhaps this is not the right way to put it, since the terms seem contradicting. Anyway, I've personally come to enjoy interacting with people who are different than me, who think differently and even value differently than me. This can sometimes lead to good-faith conflict akin to what's seen in games. Imagine a policeman who has caught a criminal, only to say "Got me! Impressive, how did you manage?" And for the policeman to say, perhaps "It wasn't easy, you're a sneaky one! You see, I noticed that ...".

I've personally observed a decrease in this "sportsmanship", but it correlates with something like intelligence or wisdom. I don't know if it's a function of intelligence or of humanity (or morality), though.

That said, my own "Live and let live", or even "Play whatever role you want and I will do the same" kind of thinking might be a result of an exotic utility function. My self-actualization has gotten me much higher on the needs-hierarchy than the greed and egoism you tend to see in any person who fear for their own survival/well-being. Perhaps this anti-molloch way of living is a result of wanting to experience life rather than attempting to control/alter it, which is another interesting idea.

Most investigations into this question end up proving something called Aumann's Agreement Theorem, which roughly speaking states that if the different agents correctly trust each other then they will end up agreeing with each other. Maybe there's some types of knowledge differences which prevent this once one deviates from ideal Bayesianism, but if so it is not known what they are.

Nope! If we're optimizing the merger, we'd see that problem coming and install whatever transhumanism is necessary to avert this.