Unused modules (?)
For example, https://github.com/flathub/org.gnome.Photos uses the "babl" module, which is already in gnome runtime 40, but when you try to build Photos without "babl", you get an error stating that babl not found. Also in https://github.com/flathub/org.gnome.gedit without a module libgit2-glib, the git plugin will not work, but it is in the gnome runtime.