I didn't find a way to reduce the 50px area around the GtK Paned because it's hard coded in the Gtk sources.
So I removed the Gtk Paned again. This is now in the 2.9 branch and so master as well.
Hello, today I had the opportunity to update LinuxCNC on this machine (it is normally not connected to the internet). I'm happy to report that the problem has disappeared!
Thanks a lot!