You can hide all windows for only one web app with ⌘-H (like a normal app). You can flip between the windows of only that web app with ⌘-` (like a normal app).
You can use any of the myriad launching tools like LuanchBar/Raycast/Spotlight to quickly launch a web app (like a normal app) and it will re-open with the last-used window positions (like a normal app).
You can press Ctrl-↓ to make the OS show thumbnails of all the windows of only that web app (like a normal app).
Finally, you can quit the web app and close all its windows with ⌘-Q (like a normal app).
Plus some I am forgetting.
Web apps are pretty shit compared to native apps, because they literally throw away all the features the OS provides for managing apps.
For any app like YouTube, Shortcut, Audible, Amazon, etc I would 100% always prefer a native app over a web app, even if it had no additional features other than being a native app.
(On Mac, I just bought this flotato thing, as it seems pretty good and promising, but I normally have been using Coherence X (a similar app) and there are others... I am not aware of any for Linux.)
Also check out Bumpr.app for Mac — it intercepts link clicks and lets you choose what browser to open them in. Would love that on Linux, as well.
Additionally, there doesn't seem to be an API for PWAs to surface menus to the system, which means productivity stuff like Google Docs is stuck with redundant in-browser menus.
Is this actually a common belief? Bookmarks are too much effort?
Rectangle, however, I can vouch for. The stock window management in OS X is the worst in the industry, but tools like Rectangle help a lot.