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've only used lxc for stuff like WordPress, haven't ever used it for GUI stuff.)
And for the original under Wine you can configure wine you not do that - or use Proton which doesn't link user directories by default.