For what I can see Flatpak handle $XDG_CONFIG_HOME in a completely transparent way: my Flatpak instance can access the same $XDG_CONFIG_HOME folder (/home/leinardi/.config/gwe) as if I run the app directly on the host. Flatpak and host app share the same $XDG_CONFIG_HOME folder with 0 code changes needed on app side. This is my current manifest.
I explained the reason why this is needed here.