I totally agree that users don’t deliberately discern between websites and system UI, or at least that the two are moving closer so that it will not make a difference. And you’re right that properly designed buttons with hover states (many OS Buttons don’t have hover states btw, on MacOS at least) have enough affordance on their own.

It’s just that we already are at a state where some buttons you come across have a hand, and some don’t. That is indeed very odd.

Isn’t this the same for websites?

I’d argue it isn’t. While there certainly are some where it fits, there’s a diverse variety of content on the web, say magazines, articles, or just styling elements on any website. There are many graphical elements that come with this content (teasers, “disruptors”, labels, visual quotes, etc…) that often have no interactivity to them and serve a purely visual purpose. On desktop you have a clear separation of UI and the content files you open inside the control frame. (such as an image in Preview, or a PDF in Acrobat).

Referring to the way others do it is appealing to authority or popularity.

Isn’t measuring against authority and popularity in a field part of our job? They often set the paradigms and preconditions users come with when reaching your system.

Plus why should, by this account, only links that are call to actions be shown as buttons? Operating Systems also use buttons for navigation within their systems. Why shouldn’t we on the web?