It's the fact that not only are Apple providing a platform to sell the product, they're also the only distribution method for the product and are slowly clamping down on the loophole of providing a "free" app that requires a subscription bought elsewhere.
To continue the flawed analogy, the Best Buy houses are clearly the best houses in most other respects in the opinion of a lot of people and it's hard for the market to apply pressure about this one specific limitation. Whether that's fine or not is basically the philosophical argument being had.
Not really. For Epic, you can buy things in Fortnite on other platforms and you get them in the iOS account. Same goes for ProtonMail I assume. The issue is that you can't advertise in the app that users can purchase the things elsewhere.
The problem and complain is much more complex once all these additional factors comes into play. It isn't so much a problem if we look at it in isolation. As in your Best Buy example, which I agree is perfectly valid.
Obviously it's not a 1-1 comparison, but Apple is giving the apps a similar platform to sell their product.