Apple supporting PWA (Progressive Web Apps) is hugely important because it enables a future where web apps can natively support browser, Mac/Windows/Linux desktop, and mobile iPhone/Android/Windows native mobile with a single codebase of open technologies.
Why is that important? By fragmenting development effort, the overall product isn't as good on any platform.
There's an app I'm making on the side to keep track of your contacts (like a personal customer management system). This needs to store all your contacts offline, because it'd be too much friction to load everyone you've ever taken notes on over the network every time you open the app.
Right now, the only way for me to accomplish that on iOS is to make a native app. This means I had to learn an entirely new technology stack (React Native and XCode), completely rewrite my views, tie everything into my backend, and go through Apple's Byzantine approval process (which I still haven't done because I can't figure out why my app compiles and runs locally but complains about libraries not being linked when I try to archive it to upload to the app store).
This is unnecessary duplication of work that could've been spent writing new features, makes it harder to add new front-end features in the future (because now they have to be added in two places), and adds a huge lag in the time it takes me to push changes to the iOS client (weeks, vs. the seconds it takes to push a change to the web client).
If apple supported PWA, I would've spent my time making the database keep a local syncing copy on the browser (with minimongo or pouchdb), and then every platform would've benefited from faster page loads and offline syncing.
Until Apple adds PWA support, I can't make as good stuff, and people can't use the better stuff.
As to JavaScript, with WebAssembly coming, there may be options in the future.
Having developed many websites and many apps, HTML and CSS are really quite terrible when compared to something like iOS' auto-layout system, or even something like a DockPanel in Xaml (WPF on windows)
However, you wouldn't want to layout a document in Xaml or auto-layout either. Different strengths for different original purposes.
Personally I feel like a non-trivial part of why "web apps" (i.e websites pretending to be apps) generally suck comes down to this impedance mismatch