IMO If the fit is tight on the pin, It's probably the larger diameter pin of the 2, or the joint protector was bored smaller then standard before tapping, and fits the other size. That is assuming the thread is not modified, It is of the same pattern,and depth. If you know it's the same thread ,the protector screws on the pin kind of loosely, and feels like it's crossthreading then the pin diameter is probably smaller.
I don't know the specific diameters or thread patterns They used, but Mike seems very knowledgeble and well equipted for them, and has every tap known to man

so his advice should be from a good source, and worth taking in.
Pretty sure The pilots should be snug in this case, atleast that's the way I prefer to do them, and believe I'm safe in saying some others do, so they snug up right at the bottom turn. I imagine that was schon's intention for using them, as well as centering & alignment. looks like a good fit to me, altough recomend cleaning them & the threads instead of trimming should they pose a problem. I would only trim in extreme cases. If both shafts were to have a problem, then look at the bore in the joint, or bent pin.
I know they do appear to be rubbing pretty hard from the marks, but from what I have seen that is normal over time with this type of joint. If It's rubbing smoothly & evenly all the way around then that's even better, because it's centering properly IMO. I like the snug fit in a cue myself. Greg