No, I meant the root diameter of the knurl. Just like threads there is a root diameter (minor diameter) and a crest diameter (major diameter). The knurl also has a crest (high point, which as you pointed out can be knocked down a bit via wire wheel or a little sanding) and a root (low point) In this case if the root diameter is too large there will be too much interference between the stud and the axle. If it is a small enough difference, no biggie. If there is too much difference you will displace metal as you press the stud in and it will build up on the shoulder of the stud and you will never get the stud fully seated. And if you already understood all that I apologize! :)
As for shoulder length, the Yukon spec was 33/64 (works out to .515) which is closest to the 9/16 you listed (at .562) which would probably work with the wheel I am using without a problem.
It is just doesn't stand to reason that Yukon would use such a bastard size. Weird. And with all the racers running those axles you'd expect they would make a long version that would pass tech at the track. The tech support guy at Yukon told me they have no such offering.