While I understand where you're coming from, I think it makes a lot of sense continuity-wise. A regular user doesn't care nor know how these apps work internally, as far as they're concerned, it's just another app. You wouldn't expect changing the settings of one of your apps to change the way random other apps work (power user tools notwithstanding).
Given I'm a developer who uses PWAs on every device, my opinion probably doesn't mean much compared to the general public.
But this means I'll never use YouTube in Web App.app, and just sounds like it's going to be annoying using my password manager (though to be fair, Safari alone makes it a pain to use my password manager)
You can try Orion browser's [1] web apps which inherit the native adblocker from Orion and have more powerful options than Safari, while still running WebKit underneath. [2]
