I know this is over a year old, but thanks for posting. I just received my builders kit the other day so it hasn't been built but I dry fitted the parts together after reading your post.
Yes, the surface of the fin can and the surface of the transition where the rail guides go appear to be in slightly different planes. Maybe a 1/16 to 1/8" difference.
Might not make a difference operationally, since the rocket transitions to a smaller diameter above the transition.
But you can build up the surface of the upper guide location by gluing on a thin square of wood to bring it into alignment. AKA a standoff.
Don't know if that's really needed though.
Might want to check for binding/scraping before final gluing.
I know I will.
EDIT: I glued the rail guides on. It slides on the rail fine. No standoff needed.