I see your point and don't doubt your knowledge of the platform, however, I don't think you've considered the fact that it might become impossible for people to even stay 100% within the App Store if companies decide to force you have to side load their app or install it from their website, think companies... like Amazon, or a Netflix-type service that could think they have enough pull-power to force that on consumers because of their business reasons.
I personally would say that from someone that just got their first Mac a few months ago, I would've preferred to install everything from the App Store but many of the utilities I needed for professional reasons weren't there. I had to do a lot of digging and researching to make sure those utilities were legit and I wasn't being scammed or getting infected with malware.
So all I'm saying is that I agree Apple goes overboard sometimes with how they handle the App Store, but some of us choose to get an iPhone because we can rely on feeling safer with the apps we install on a device that mind you, never leaves your side and has all of your personal things on it.
And just as a side note, encryption interoperability in messaging sounds like a nightmare and I'm not sure what purpose it would have since you can install those apps anyway.