I've long given up on keeping a clean home folder because so many software do this and keeping it clean is a constant chore. Now I just make a real_home folder in my 'home' and put all my actual stuff there. They can use the ~ landfill
I just never look in ~
I stopped using that software no matter how painful it was some games included. I wanted to play BG2 and the remake from GOG just litter the Documents folder even when running though Wine. Well, no game for then. Pity. I want my computer to serve me and to have my own files where yo want them.