Applications installed with Flatpak are keeping user data and configuration under ~/.var/app/ (see Wiki and documentation).
I would like the applications installed with Flatpak to reuse the configuration and data left from the system versions of the same applications. That is, I want them to keep user data in ~/.local/share, ~/.config, ~/.cache, instead of under ~/.var/app.
At first I was hoping that configuring environment variables XDG_CONFIG_HOME, XDG_DATA_HOME, XDG_CACHE_HOME could suffice, or that it could be enough to start the application with --filesystem options:
$ flatpak run --filesystem=xdg-config --filesystem=xdg-cache \
--filesystem=xdg-data <application-id>
However, this did not seem to work.
What is the correct way to make Flatpak applications reuse user data and configurations in standard locations?