I just treat ~ as a system-owned configuration area, and put my actual files (documents, photos, etc.) in a completely different hierarchy under /.
"/home/${USER}" for whatever junk programs are going to stick there, "/home/${USER}/home" for my "real" home directory.
I have been doing this for decades. My files are in a sub-directory of $HOME. It also makes it very obvious when a piece of software does not treat your $HOME with respect.
You could write a kernel module, then, that just hides certain symlinks from you (which is effectively what this module is).
On Windows this was always easier because, for some reason, most everyone respected %appdata% compared to XDG_CONFIG_HOME, but also because hidden files wasn’t just a naming convention but an actual separate metadata flag.
Always... Except for the decades before this became common. Never a bloated C: root directory. Microsoft even had games store stuff in My Documents\Games at one point. My Documents was a user dir that saw a lot of abuse over the years.
They still have that, it's just `My Documents\My Games` now. And Visual Studio makes a folder in My Documents for every annual release. And…
Yes, as in there’s no reason Linux can’t clean up its game the same way.