A lot of flatkill.org’s statements are made to incite fear in the Linux community. Given that all Flatpak packages and application build scripts are available and able to be edited by anyone, the appropriate response is to educate on why this is a problem, and then fix it. The way that flatkill.org approached this issue says a lot.
As long as people don't use Canonical's non-FOSS snaps instead. Permissions needs a major update for linux anyway - access to /home/user needs to be heavily restricted, and XDG standards for ~/.config etc enforced or invisible for programs. If wine tries to make or access ~/.wine, it gets caught and put in ~/.local/XDGjail/.wine or something. Stop letting unprivileged processes access ~/Documents!