The VR DOES NOT run through the ballast. But the wiring CAN be problematic, especially if factory, and especially if ithas not been well maintained. The typical voltage drop in the "run" line causes the VR to OVER charge (over voltage) because the dark blue "ignition run" line with inherent drop, providing low voltage to the VR, which then ramps up charge voltage to compensate.
One workaround is a relay. Electrically cut the dark blue "run" line where it enters the engine bay, out of the bulkhead connector, and BEFORE it branches off. Use the firewall end to trigger a relay, connect the engine bay cut end of the dark blue, to the switched contact, and feed the relay power off the big stud on the starter relay, through a fuse or breaker.
