Someone needs to sue Apple for this, and the truth will be revealed when the case enters discovery mode, when Apple internal communications on this are laid bare
For example, Apple prioritized service workers over web app manifests (which BTW are not yet a W3C recommendation). I can only assume this is partly because there have been so many failed attempts at static web app manifests in the past. Them prioritizing other features for earlier release doesn't mean that Web App Manifest support isn't in active development ( https://bugs.webkit.org/show_bug.cgi?id=158205 ).
1. Binary WebRtc data channel messages
2. Browser notifications that a PWA can use
3. Web App storage beyond 50MB, and guarantee that the OS won't whimsically delete storage, despite being below 50 MB
4. You've already cited Web App Manifest
There's probably a ton of other W3C standards not in compliance, but the above list is pretty damning.