I almost (ugly story) put mine on but had to stop because they will not fit with a Rostra CC actuator mounted under the left fairing. But I did get the bars themselves installed and the threaded shaft ended up similar to yours although maybe another turn or turn and a half deeper. Then again, I did not install the washer so that might make a very small difference.
The spacer that goes on the left hand side of the engine mounting bolt is not symmetrical, and the counter bored side has to face out to get the nut on the stud as far as possible.
While the threads do not come all the way out to the end of the nut, it is not a conventional nut and has a long, threaded shoulder that also engages the bolt. So it is not imperative that the stud reach all the way through the nut in this case because the nut is so much longer than a conventional flat nut.
As far as the stud being all the way into the frame, if it hangs up on the hex it will be quite short and I do not think you could even start the nut on the other end. So the hex must be timed correctly to even assemble everything I believe.
Brian
Well, I will try and keep this brief. I decided to take the nut off and try to rotate the bolt, did not happen. You guessed it, the right cage had it binding due to the angle. That left me with two options, remove the tupperware or loosen the bolts through the vents. I was fortunate to use a swivel and get them loose enough to allow the bolt to be pushed through. I rotated the bolt and pushed again and same threads showing. Inside the right canyon is a lip that stops the head of the bolt from going through. (wish it was a larger lip because only the points on the bolt head are keeping it from going through, looks like an exact size washer would help but this would allow even less threads to be engaged on the left side) I measured that depth minus the head thickness and the bolt is inserted as far as possible and the canyon is in the hole pressing up against the bike. I deducted the bolt is seated as far as it will go. As stated the hex shape on the shoulder's bolt keeps it from spinning when tightening so that verifies it is properly installed. I torqued it to 44 ft/lb and my bike looks just like the one posted in the initial part of the thread. If anyone has less threads showing I am guessing they are using more than 44 ft/lb. I can tighten it more but do not want to risk any problems. I look forward to other replies with much interest. I spoke to Ryan who was helpful. I suggested using a head like the factory bolt to allow turning while in the channel of the canyon cage. Also it appears that the nuts are different between Ryan's photo and ours posted above.
