Flatpak's FAQ claims the following:

How does Flatpak relate to freedesktop.org technologies such as desktop files and appstream metadata?
These standards are incorporated as mandatory parts in the flatpak definition. By relying on these standards we are building on years of investment and support under Linux.

This doesn't seem to be true.

One of the standards Flatpak violates is the XDG base directory spec: It incorrectly places files outside of the specified XDG_CACHE_HOME, XDG_CONFIG_HOME, XDG_DATA_HOME directories, by creating and populating a .var directory in $HOME.

I think the documentation could be improved by dropping the "freedesktop.org technologies such as ..." part, and explicitly listing both the standards adhered by Flatpak as well as those standards Flatpak chose to ignore.

I believe this could reduce user confusion as users might expect that an application formerly named xdg-app follows the same-named standard.