You might think, "Ah-ha, web apps!" But no, Google can still casually destroy you there. Or you might think, "Ah-ha, desktop apps!" But the OS vendor can casually destroy you there.
Casually? The amount of effort and goodwill, say, Microsoft would need to spend to prevent me from installing $PROGRAM on my computer is significantly higher than the amount of non-effort a single extension reviewer would need to expend to click "no" arbitrarily because they are having a bad day.
How would Microsoft do it? Add legit software to Defender? Ship a Win10 update that disables a key API call $PROGRAM uses? Add "if program == $PROGRAM then exit" to the CreateProcess code? All possible, none casual. To the best of my knowledge they've never done something like this. I'm less deep into Apple land but I expect something similar holds on macos.
To its credit (though not everyone agrees), MS has spent a lot of effort making compatibility shims, basically doing other people's work for them, but they have no such obligation.
This is a different class of problem. In this case, a gatekeeper is asking you to use their service to distribute software through their channel, and that channel is governed by vague rules that may, in fact, be enforced on a whim. Further, the gatekeeper isn't being clear with the rules, and why you may have run afoul of them.
You sound like someone who's made the mistake of supporting Apple
Well, considering how hard Apple tries lately to make sure every piece of macOS software goes through them one way or another...
My point is not that they can't do it, my point is that they can't casually do it. It would be Real Work and it would risk major backlash.
That's unfortunate, but it is how the software market has worked thus far. Platform owners have massive power over those who build on them. For it to change, the market fundamentals will have to change. People thought the internet would change things, and it did - instead of one monster, we now have several, each with much more reach and control.
As far as actionable advice, well, starting a company isn't easy or formulaic. All I can recommend is look for niches where you'll be hard to dislodge and avoid situations where you have asymmetrical dependence on an entity that has no reason to care about you.
That won't matter if 60–70 % of the users are on that single browser.
At the moment the issue is the app store concept; it is designed to be a choke point, it is designed to be obscure, and it is designed to casually destroy software the store owner doesn't approve of.
(What is the status of Microsoft's app store, by the way?)