git works great with Altium binary files... yeah you can't merge branches, but that's not really how you do PCB design anyway (and even with ascii pcb format, trying to merge 2 different versions of a PCB file with 2 different areas of different changes would be hell. PCB ASCII format is hardly source code... :-)
speaking of merging pcb variants, Altium itself does have a visual pcb diff tool, but I've never been unlucky enough to have to seriously use it to merge different branches of a PCB design, and I hope I never am...