It's not harmful to swap the VR sensor wires. Often times we do have to do that because for whatever reason the OEM decided to run the sensor backwards from common convention. If you check the signal with an oscilloscope the signal should rise more slowly than it falls.
That's a rather crazy Subaru trigger, but you can see the distinctive shape of the VR signal well (both top, crank trace and bottom, cam trace)
If the rise is steep and the fall is more gradual, just swap the wires.