[…] IIUC gtk_application is based on g_application which is linked to Gnome (again IIUC, no guarantees its right).
I don't have any clue that this is true at any level :) GApplication is the base, yes, but it's from GIO, which we (and more importantly, GTK) use anyway. GApplication is the non-GUI base, GtkApplication is an additional layer for GTK stuff.