I think most people are okay with software such as OpenSSH keeping its long-existing conventions. In the same way I don't think a lot of people mind ".bashrc" being where it is. It's manageable if there's just a few and they're well-known.
However this "exemption" does not and should not apply to anything newer. Things like Cargo, Snap, Steam, Jupyter, Ghidra, Gradle, none of those should be putting their stuff (especially temporary junk) directly and unsegmented into $HOME.
At some point I had more than 50 different dotfiles and dotfolders in my $HOME. It was unwieldy and nasty to look at. I couldn't even figure out what created some of those files because they were so generic.
Plain $HOME as the dumping ground simply does not scale beyond a select few.
It's been a while since I used Windows, but I remember the "My Documents" folder being trash pile of configs, save games, data files and whatnot, making it the worst place to actually store your documents.
Windows-oriented developers bring that mess to Macs, too, and it's incredibly aggravating. For over 25 years, Apple has had Documents/Pictures/Movies/Applications/Downloads/etc folders under the user's home folder, and convention is predominantly that you never put non-hidden files or folders in the user's home directory. And you don't put application configuration in Documents, because that's what ~Library is for.
Then ignorant developers who don't care about the platform throw random configuration folders in ~/ or ~/Documents, or think their app needs a central workspace folder for all of its projects, instead of letting you manage your own damn files.
It's just plain lazy devs. They do that crap on Windows too despite having conventions for where the stuff goes since Windows 98 (though Photos and Videos folders were introduced with XP, and Game Saves with Vista).
The folder for config is even older. CSIDL_APPDATA has been able to be used to get the path to the AppData folder since the update for Windows 95 that added Internet Explorer 4.0.
However this "exemption" does not and should not apply to anything newer. Things like Cargo, Snap, Steam, Jupyter, Ghidra, Gradle, none of those should be putting their stuff (especially temporary junk) directly and unsegmented into $HOME.
At some point I had more than 50 different dotfiles and dotfolders in my $HOME. It was unwieldy and nasty to look at. I couldn't even figure out what created some of those files because they were so generic.
Plain $HOME as the dumping ground simply does not scale beyond a select few.