First off, THANK YOU for posting that video... very informative. I've done a fair bit of reading on the subject and have rebuilt/upgraded (cheaply) forks and even after all this I feel like I blundering in the dark most times when adjusting my suspension.I do not agree. The forks should be aligned so that they are at equal hight. If the axle can turn easily does not matter. Fork hight explained by Traxxion Dynamics, look at 9 minutes out in the video.
If the two forks are identical in length - and they should be when uncompressed - then by adjusting the heights so that the axle will slide in means, effectively, that they are aligned. If you then measure the amount exposed above the triple I think you'll find that unless there is an issue with fork assembly... something like an improperly seated seal... then this measurement should be the same side to side.
Any way you set them up which yields an axle which will not slide easily through both forks is going to give you potential problems... starting with getting the wheel installed!