Are you speaking as a user? I'm speaking as a dev. Of the applications you mentioned only a couple actually use the Win32 controls (like Notepad++) and they custom render them to get dark mode. That's a lot of extra work they had to do, essentially draw the whole look themselves.
Chrome is not native. FF is not native. Qbitorrent is not native (it uses Qt, right there in the name). Signal is not native, it's a web page bundled with Chromium (aka, an Electron app). WinSCP only this year actually started using the right font! But at least that one is native I'll give you that.
The GitHub you sent doesn't really have anything to do with the discussion.
Chrome is not native. FF is not native. Qbitorrent is not native (it uses Qt, right there in the name). Signal is not native, it's a web page bundled with Chromium (aka, an Electron app). WinSCP only this year actually started using the right font! But at least that one is native I'll give you that.
The GitHub you sent doesn't really have anything to do with the discussion.