Mine displayed mild front brake torque oscillation at its last MOT, and after being told that I could only just feel it, just as I came to a stop. There is variable drag on the discs if I rotate the wheel by hand with the brake barely applied (zip tie), but I was not able to see any runout at that time. It doesn't really bother me, but I could try that pen trick or using a proper gauge.

I suspect you'll only notice the pulsation if you run out of float in the buttons, so a misaligned axle and fork tube could do that. Variations in the deposits on the discs around their circumference would cause pulsing, too. Unfortunately, I started using new pads (different material) and messed with the forks at about the same time...