An independence vote should maybe not just be a simple majority, I think at least more than 2/3 like what is usually required for a change in consitution would make sense. But other than that, you're just describing how democracy works. Just about no western country is a homogenous group. There are always people of wildly different background and with wildly different views and they often get rules imposed on them they don't like. This is already happening right now. So are you against current countries running democratically as well? You're arguing that a presumed minority of non-independence voting Catalonians will feel disenfranchised, but you're at the same time perfectly fine with the presumed majority of Catalonians feeling disenfranchised right now? How does that make sense? If you're arguing for minimizing disenfranchisement, your point is clearly inconsistent.

The only way to minimize those frictions for a society that can only function in organized groups is to make the units of self-determination relatively small. So yes, I absolutely think that every geographical region that wants to hold an independence referendum should do so. Why not? There's nothing speaking against that. If your concern is that many people might have rules voted on them they don't like than you should be for each individual's votes counting as much as possible.

Also, there's nothing saying that if a country goes independent, there can't be some transitional rulesets, where people can potentially switch nationality, lived by mixed rules for a while etc. I absolutely think that in such cases there should be some rulesets in place to ease the transition and give people some choice. But all that only makes sense if we have some consensus about where the majority of a region wants to go. Which Catalonia isn't even allowed to officially find out where they stand and start negotiating about that.

Maybe it could be gerrymandered to shut up the whining minorities?

How do you gerrymander a region deciding about its independence? If the regional borders for a referendum are "arbitrarily" drawn (all borders are) in a way that 95%+ or whatever support independence, that just means that you just minimized the amount of people who would feel disenfranchised by that decision, which is what you made your main point of concern. Gerrymandering only can be done (maliciously) when te seats/votes for a plurality of administrative units is determined in a first past the post voting system. None of that has any relevance for or applies to an independence referendum.