This doesn't happen on Android, so don't worry too much about it. I can bet my 2 cents on that 99% of users will only use app stores even after this regulation and Apple has a power to make it happen. Of course Apple will need to spend some of its energy on suppressing real competition but that's not what customers need to worry about...
Any of this is already possible on MacOS, Windows, and Android. It's not actually so wild as you're making it out to be. Just ignore the software merchants you don't want to affiliate with. I don't like Valve, so I don't install their 'appstore' Steam. That means I can't buy games that are only sold on Steam. Big whoop, it's a consequence I accept of a decision I am free to make or reconsider. Life goes on.
Yeah, even the ones run by major tech players- the Amazon and Samsung Android app stores, are really just there to serve their own devices. They don't contain any exclusive apps that are forcing Android users off of the Play Store for.