I usually treat an app putting stuff into $HOME with no reason to change that as a reason to not use the app. I've genuinely switched software multiple times because of the old one doing this.

I also suggest you try xdg-ninja, which automatically scans your home directory and shows which of those directories you can change to a different location:

https://github.com/b3nj5m1n/xdg-ninja

I have a big shell config file that sets proper locations for all sort of programs I use:

https://github.com/flexagoon/dotfiles/blob/main/dot_config/f...