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
With most "native" platforms you can have a WYSIWYG UI editing (because those markup languages were designed with that in mind). You visually define the layout (with mouse/trackpad), drop components there, and it's all nice and easy to use. Surely, you can code your UI as well, but to best of my knowledge no one in their sane mind does this, unless they have some very good reasons.
With web apps (progressive or not), the usual approach is to code stuff by hand, and see the results in the synchronized preview pane (or nearby browser window), patching the code until it all fits. Even if there's some tool/IDE somewhere that would let me bootstrap a React/React Native/Elm/whatever app with a mouse - by dropping a button on a pane and connecting an event listener with another mouse click (like I had it in Delphi, 15 years ago), I think it would be an exception, not a rule.
Or maybe I'm just unaware about how things are really done and have false beliefs, heh.