I'd say Windows is a bit more fragmented UI-wise than Linux, even if you remove Qt from the conversation entirely. There simply hasn't been a strong notion of "this is how a Windows app looks" since the, say, Win 98 days between multiple different generations of MS-blessed designs, the skin-heavy era and a myriad of toolkits. The classic "Windows app" design in my mind is Notepad, and few apps look like Notepad. I admittedly don't use Windows heavily, but the few apps I use occasionally inside a Windows VM or on the dual-booted Windows on my laptop all sport widely different UI appearance:
- iTunes (built on a port of some of Cocoa I think)
- Spotify (custom UX, also on Linux - using Qt - but I don't bother)
- Steam (custom UX, own toolkit - also on Linux)
- EA Origin (custom UX, made with Qt)
- KakaoTalk (custom UX, I think using a native toolkit though)
- LINE (similar to Kakao)
- Telegram (custom UX, built on Qt - actually this runs fine on Linux, but I keep it in the VM alongside KakaoTalk because it's the same use case)
- Firefox (custom UX, with native-ish theming by its own XUL toolkit grabbing stuff from Windows APIs)
- Chrome (custom UX, built on a custom toolkit called Aura with some Windows exceptions)
- Kodi (custom fullscreen UX)
All of these are apps with user numbers in the range of hundreds of thousands to tens of millions, and they're all unicorns. (You may never have heard of KakaoTalk or LINE, say, but both have 50+ million desktop installed bases.)
Some of the above (Telegram, Firefox, Chrome, Steam, Spotify) show up on Linux just the same, no better or worse. Outside of that, most apps people actually use on Linux:
- KDE/Qt apps, which import a lot of standard structure from kxmlgui and DE settings (e.g. dialog button order, standard dialogs) from Qt's QPA plugins
- Gnome apps, which follow a strongly defined HIG
- Non-Gnome GTK+ apps imitating the Win98-style HIG for the most part (which overlaps a fair bit with the kxmlgui standard structure)
Sure, there's a long tail of other toolkits on Linux (just as on Windows), but my argument is basically: Going by the most-used apps, Windows and Linux suffer this problem (if you consider it one) to a similar degree, but Windows slighly worse because outside the apps showing up on both platforms, the remaining popular Windows apps are more fragmented UX-wise than on Linux with its three broad categories.
Heck, Windows 10's bundled apps are fragmented UI-wise to a much greater degree than any competing offering due to the classic/Metro divide.
It's an utter mess. An interesting question is whether this messyness hasn't had some benefits (like allowing app designers to iterate and innovate individually, with no concern for following a system HIG, allowing the overall platform not to fall behind the curb). But arguing the mess isn't there is very strange to me.