Flatpak apps can be uninstalled without leaving a trace: flatpak uninstall --delete-data com.google.Chrome
But you might need some global overrides to make all apps write their configuration into ~/.var. Personally I globally revoke apps the permission to access filesystem= host, home, xdg-config, xdg-data.
That was actually the main reason that made me switch to Flatpak. Previously I used VMs to try out software, but with Flatpak I know that I can get rid of the application completely.