Linux does have some weirdness still where apps occasionally put files in the same directory not just under the same directory. You have the same separation in windows as in linux mostly (user data, app data, app binaries, settings, startup ...) but on windows all of those are directories per-app under the folder in question. Like %ProgramFiles\MyApp, %UserProfile%\AppData\Local\MyApp or %ProgramData%\MyApp for example.

Matter of taste I guess. I always disliked the linux way and prefer clear separation of concerns.

Same. Especially sharing any binaries between applications. For a single user desktop system it just seems like a backwards idea.

btw. with msix or flatpak things did change significantly. well microsoft does it a little better because production msix create a kind of sandbox appdata/storage.