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 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.
(I've only used lxc for stuff like WordPress, haven't ever used it for GUI stuff.)