A lot of the anti-Apple arguments I see here seem to have an element of ideological fixation. IMO the practicalities of the real world are always more involved than an ideological black/white distinction, and just as you said here there are always tradeoffs on different fronts. Openness instead of a walled garden is nice, but how far can you go with it? If you think about it, every company is essentially a plutocratic organization or even somehow military-like, where most important decisions are made by the few elites at the top and passed down, and people are quite fine with it.
Of course the argument here seems to be that Apple is gradually becoming an almost "public good", while if you're unhappy with a company you're working at, you can switch. But then again if there are better alternatives to Apple, nothing theoretically prevents the users from switching. I have been using Android since forever but this year I'm switching to iPhone. The touted "freedom" simply is not evident in most scenarios during my daily phone usage, and I'm fed up with a lot of downsides of Android (ironically, it's hard to think that being tracked by countless potentially malicious apps offers you more "freedom" than living in Apple's ecosystem), also Google is not known to be exactly friendly to developers either and it can be even more Kafka-esque to appeal a ban, apparently.
To maintain the standards of a system, sometimes the maintainer has to get hard, and this would result in them occasionally cracking down on false positives. Still, it's similar to how a society cannot function without an actual enforcer of rules, which is the police. As long as there is a mechanism/will to redress the false positives, it's much better than a system where there's no control at all. Of course, if you say you're a hardcore libertarian and are fine with living in a society without any policing and would rather protect your own interests yourself, no problem and you can always go with the most liberal phone OS out there. But most societies can't realistically function that way nor do most people wish it that way. The app ecosystem is similar in this sense.