As the author identifies, the idioms come from the use of system frameworks that steer you towards idiomatic implementations.

The system UI frameworks are tremendously detailed and handle so many corner cases you'd never think of. They allow you to graduate into being a power user over time.

Windows has Win32, and it was easier to use its controls than rolling your own custom ones. (Shame they left the UI side of win32 to rot)

macOS has AppKit, which enforces a ton. You can't change the height of a native button, for example.

iOS has UIKit, similar deal.

The web has nothing. You gotta roll your own, and it'll be half-baked at best. And since building for modern desktop platforms is horrible, the framework-less web is being used there too.

The author may have identified that "the idioms come from the use of system frameworks", but they absolutely got wrong just about everything about why apps are not consistent on the web (e.g. I was baffled by their reasons listed under "this lack of homogeneity is for two reasons" section).

First, what he calls "the desktop era" wasn't so much a desktop era as a Windows era - Windows ran the vast majority of desktops (and furthermore, there were plenty of inconsistencies between Windows and Mac). So, as you point out regarding the Win32 API, developers had essentially one way to do things, or at least the far easiest way to do things. Developers weren't so much "following design idioms" as "doing what is easy to do on Windows".

The web started out as a document sharing system, and it only gradually and organically turned over to an app system. There was simply no single default, "easiest" way to do things (and despite that, I remember when it seemed like the web converged all at once onto Bootstrap, because it became the easiest and most "standard" way to do things).

In other words, I totally agree with you. You can have all the "standard idioms" that you want, but unless you have a single company providing and writing easy to use, default frameworks, you'll always have lots of different ways of doing things.

Well, and worse, Windows was itself a hive of inconsistency. The most obvious example of UI consistency failing as an idea was that Microsoft's own teams didn't care about it at all. People my age always have rose tinted glasses about this. Even the screenshot of Word the author chose is telling because Office rolled its own widget toolkit. No other Windows apps had menus that looked like that, with the stripe down the left hand side, or that kind of redundant menu-duplicating sidebar. They made many other apps that ignored or duplicated core UI paradigms too. Visual Studio, Encarta, Windows Media Player... the list went on and on.

The Windows I remember was in some ways actually less consistent than what we have now. It was common for apps to be themeable, to use weirdly shaped windows, to have very different icon themes or button colors, etc. Every app developer wanted to have a strong brand, which meant not using the default UI choices. And Microsoft's UI guidelines weren't strong enough to generate consistency - even basic things like where the settings window could be found weren't consistent. Sometimes it was Edit > Preferences. Sometimes File > Settings. Sometimes zooming was under View, sometimes under Window.

The big problem with the web and the newer web-derived mobile paradigms is the conflation between theme and widget library, under the name "design system". The native desktop era was relatively good at keeping these concepts separated but the web isn't, the result is a morass of very low effort and crappy widgets that often fail at the subtle details MS/Apple got right. And browsers can't help because every other year designers decide that the basic behaviors of e.g. text fields needs to change in ways that wouldn't be supported by the browser's own widgets.