This has been mentioned a few times before, but I couldn't find a relevant bug for it.

First, here in the original discussion around the org.freedesktop.FileManager1 interface: http://lists.freedesktop.org/archives/xdg/2011-May/011971.html

Then, during the Nautilus patch review: f01e2e9b

Finally, in the context of Firefox using the interface: https://bugzilla.mozilla.org/show_bug.cgi?id=417952#c17

Now it has come up in gnome-photos#7 (closed)

The problem is that Nautilus ships org.freedesktop.FileManager1.service.

In the traditional non-Flatpak case, this means that no other file manager can ship that file and be installed together with Nautilus because their paths will conflict. Hopefully, nobody tried that because, it also means that if Nautilus is installed then it ignores the user's default file manager setting (inode/directory handler) and hard codes Nautilus, and avoiding that was the whole reason to create the org.freedesktop.FileManager1 standard. In short, it's pointless. :)

With Flatpaks, an application can only export services with bus names prefixed with its application ID. So, org.gnome.Nautilus cannot export org.freedesktop.FileManager1. Therefore, one can't use Nautilus through this interface if Nautilus is Flatpaked.

A better way to implement this (as mentioned in the above URLs) would be to have gnome-settings-daemon front the D-Bus interface, and then forward the calls to whichever application is set as the default file manager (inode/directory handler).