Hello! I've found that gtk+:3 is using libepoxy to load OpenGL library, so there is no need to have mesa dependency. I cannot find any mentions of libGL in gtk sources and compiled libraries. Also, Ubuntu and Fedora packages does not have any mesa deps.
Probably, for wayland, gtk+ is also missing media-libs/libepoxy[egl] dep, but I'm not 100% sure.
Right now I have system with gtk[X] and without libGL.so and libGLX.so, and everything works, including gtkglarea example, firefox, chromium, other GTK apps.