Well the 'not-dockable' base problem in the Earth system isn't related to GC, since GCv1 has nothing to do with the docking procedure...
Now the missing Starbase 12 station in the Starbase 12 system, and the Drydock in the Drydock system is a problem with GC, which that script I mentioned fixes. I attached it here, just put it in the folder "scripts\Custom\Autoload" of your BC installation.