I totally agree that PWAs count as apps and are eligible for end-to-end encryption (as long as they don't dynamically run code coming directly from a server). I don't know exactly the story on iOS though, I just know that I like "native apps" better then PWAs, but that's a preference.
> I'm just trying to condemn Apple's preferential treatment of native apps
Are they actively working against PWAs, or are they refusing to spend resources supporting another technology? I could understand that they don't want to go out of their way to add new "features" they don't care about.