The App Store makes Apple billions.
By locking you down they get the ability to get a cut of your app.
If you could install a mobile app directly from the web, they're cut out of the loop.
They also can't use it as a system of control to block apps they dislike.
I agree that there are times where this might be valuable and that there are APIs that you might want to restrict but then have a fair policy about which apps you block and also have a way to get PWAs approved easily.
Also, it's VERY expensive to get your app there due to their use of Dunn and Bradstreet.
You either have to pay $1000 or you have to wait 1-3 months until your company is approved.