Look at how older versions of Word, Excel, and Visual Studio worked. The tool trays stay consistant as you move between document windows. The entire application is minimizable and quittable together as one.
Photoshop still uses this metaphor. In the ealry and mid-2000s, Photoshop on Windows had a window for the application separate from the documents, but on Apple OS9 and OSX, the only representation of the application itself was in the menu bar. Document windows and tooltray windows both floated in the same desktop space as every other window.
I haven't checked on the GNU Image Manipulation Program, but I seem to remember it retained the same "no application window, tooltrays and doc windows exist in the DE" metaphor for much longer than Photoshop.
There is also a difference in the way that Chrome renders tabs in the window title area. That's a part of the UI chrome that one would expect to be in the perview of the UI toolkit, but Google took it on themselves.
https://en.wikipedia.org/wiki/Tab_(interface)
Don Hopkins himself can enlighten us about it (NeWS) better than me literally anyone in this thread, jut wait.
This goes towards something that I've felt for a little while: at some point in time around the early 2000s, operating system vendors abdicated their responsibility to innovate on interaction metaphors.
What I mean is, things like tabbed interfaces got popularized by Web browsers, not operating systems. Google Chrome and Firefox had to go out of their way to render tabs; there was no support built into the OS.
The OS interfaces we have now are not appreciably different from what we had in the early 2000s. It seems absurd that there has been almost no progress in the last 25 years. What change there has been feels like it could have been accomplished in user-space, plus it doesn't get applied consistently across applications, thus making it feel like not a core part of the OS.
MacOS in particular was supposed to an emphasis on the desktop environment being the space of window and document level manipulation, as exemplified by the fact that applications did not have their own menubars. All application menu bars were integrated together at the top of the screen. Why should it be any different with any other UI organizational feature? Should not apps merely be a single window pane, accomplishing a single thing, and you combine multiple apps together to get something akin to an IDE out of them?
Well, I don't know if they should be. But they can't. Because OS vendors never provided a good means to do it. Even after signalling they wanted it.