I like walls of text :)
That was a surprising conclusion. :) Made me smile certainly. I'm afraid biology / zoology are not my fortes though ;)
I'm reading your post and wondering if this is how people often feel when they read mine... funny that.
So, if I understand correctly, you are first saying conflict is inevitable due to different value systems. I cannot agree more and that is basically the similar premise to my OP - conflict being exactly what I proxied for with the "interminable arguments".
Then you are asking something I don't really understand, but perhaps I don't have to because you used it to highlight the paradox of tolerance coexisting with wanting to change others so they agree with you. And I think that's your actual point there?
I also agree with that, although I would point out that this approach is not universal. There are those that go for destruction / subjugation as a more "economical" approach. And this might be "rational": instead of spending a week convincing Urgh to give me half his fish for half my fruit, I can just knock them in the head and take it. I think someone that makes this point very well is a guy called Azar Gat. But I digress. What I describe is obviously not tolerance in any way. The other intolerant tolerance, with attempts to convert others, is at least a step towards a more ideal tolerance.
Anyway, I agree this paradox is a real dynamic, and I agree with the point that underlying this desire to convert others is an almost instinctive desire for unity in the social group with associated punishment of defectors.
Now getting to the final point (I'm not counting the one about the rats) I think your question is: Should we try to have one universal set of meta rules (I think calling this homogeneity is somewhat misleading by the way - as you mentioned yourself only part of the whole value system might require uniformization), or should we rather segregate somehow into compatible subsets.
My personal answer involves what is called the non-aggression principle as the meta rule, with that principle deriving from a premise of fundamental equality of value of each individual human. I agree though that in practice segregation happens at many levels, from the formation of families to the formation of countries. I think the two can be mostly resolved without contradiction. Although one can always postulate meta conflict a la Godel.
Come to think of it this goes back to the point I made about exclusion. There is a difference between choosing to associate preferentially with A, B or C, with consequence that D, E or F might be harmed. And choosing to harm D, E or F. This last is what I think is bad exclusion, whereas the other is just life. But there are many folks that look only at the outcome of harm without the consideration of either intent or propriety of agency. Which is ironic actually, but I digress again.
So now that maybe (hopefully) my answer to your question is clearer, I'll restate my earlier point you replied to. Not sure it's needed, but you can judge what to reply to - if anything ;)
When I said exclusion of a limited kind is implied by choice and limited resources I meant precisely the kind of natural segregation we see in the world and you mentioned. For the lowest level of social example: I am limited in my existence, and I should be able to choose to spend as much of that with A if I so wish. Because I love them. This means I am excluding myself from being with others, and maybe they will hurt because of my choice (and my finite existence - the incoherent fantasy about cloning / multiplying oneself is borne here). This is the same principle I apply at other levels, it all deriving from self-ownership.
When I said there is a different kind of exclusion I was referring to bad exclusion. The intolerant kind of actual war / conflict / aggression. I was not even referring to the intolerant tolerance of activists / missionaries - that's a grey area in between mostly. Any attitude of entitlement to something that is not ours I consider much more exclusive. Pun intended because this kind of bad exclusion is the root of privilege. Entitlement to what is actually mine is not privilege, it's self ownership and it's a basic human right.
So, to avoid this coercive exclusion, I don't think we require homogeneity - we can all be different as long we respect that diversity per the kind of rule system you mentioned. I think most of my takeways in the OP are along those lines... But to avoid the first kind of exclusion, where we make choices and have preferences and that causes inequality - this being its commonly given name ;) - even supra-fundamental human equality is not enough, we could all be perfect hermaphrodite clones but with limited resources some would get, and some would not get. That there is an actual utopia, as in, it's inherently unattainable - not due to imperfect human nature, but due to inhuman external realities.