The reality is that the decision to use alternate stores will not be from user choice - it will be from large internet companies telling them the only way to get Facebook is via the Facebook store, to get Fortnight is from the Epic Games Store, to get Netflix is via the Netflix store, etc.
And the purpose of these stores will be to skirt Apple requirements on apps in their store - not just payment, but things like network traffic surveillance.
These stores will also not be pitched by companies based on informed user decisions. They will be pitched in order to get users to sign up in whatever way they can drive taps through consent screens.
So unfortunately to remain a user choice, there needs to be a strong disincentive for parties to force a customer into a third party store, but not so strong that it looks like antitrust.
Google Play for instance has tons of "Play Services" which are not available to apps from alt-stores.
The Mac has certain security settings which can only be disabled through a process requiring a reboot and command-line action as a way to limit vendors from driving customers through disabling essential security features without proper education.
Mac applications are also notarized, so whether they are downloaded through the official app store or a third party channel they can be scanned for static issues and revoked after the fact as malware in the case of dynamic issues.