I think Apple made a serious miss-calculation there. If they're being honest, and removed web apps because they are technically difficult to implement, they should have said something along the lines of "we are working on this and will disable it temporarily to avoid penalties".
But I suspect it's got nothing to do with that. Web apps can run native code with WASM and it would only be a matter of time before someone (google?) releases a "browser" that allows you to run native Android apps. Or worse, native iPhone apps... bypassing Apple's Core Technology fee since it's "just a webpage".