These days it is damn hard to tell where Gnome ends and Freedesktop, never mind Fedora, begins.
All too often it feels like Gnome and Freedesktop is out to fix "problems" that only exist within Fedora, in the process turning every other distro they touch into a Fedora clone.
It is developed by people involved in Gnome, but it's desktop-independent. http://flatpak.org/faq.html#Is_Flatpak_tied_to_GNOME_