To make it line up on a schon in production you would attach the shaft, then use the logo to align the butt cap.... but no I dont think it is meant to line up. I have some schons that are close, and some that are not.
Danny Janes of Joss on the other hand, use to make sure the joint collar and shaft collar lined up on the old gold letter customs. I think that is where the "urban legend" came from about schon. Evan doesnt like anyone but himself making shafts or doing work on his cues, so he started marking the shafts (first he did the shaft collar, then the vertical logo on the shaft wood itself) to make sure a shaft that came back to his shop for work was one of his.
Hope this helps
Chuck