I think more the limitations imposed by the gnome library that gets installed for the Gimp flatpak.
/var/lib/flatpak/runtime/org.gnome.Platform/x86_64/3.28/some-long-string/files/lib
Kubuntu 16.04, I can get the GTK version, (one I compiled for Gimp 2.9.9) running by slipping more-than-a-few library files into org.gnome.Platform
I am sure that is not the way to do it, but it works here.
Tried the QT version but a step too far, that runs into conflicts.