How I read their wording as a cuemaker is this. "The long alignment shoulder will help keep you from cross-threading the shaft on the joint pin."
I'll have to disagree with you Chris. As a cuemaker, I read it entirely different. A layman would read it as previously stated.
Seeing it as a cue maker, you first put the pin into the shaft. The "long alignment shoulder" plays absolutely no part in the initial alignment. The "long Shoulder" comes into play perhaps at the last 1/3 of tightening it up because that's when the "long shoulder' will first see the alignment hole. You have to get there first before it can "help".