I don't know from maneuvering panels to accommodate contour cutting but I do know about clearances necessary to do the job.
The only clearance you need to maintain is maybe 1"-2" between the pressure rollers and the outermost registration marks on the outside edges of the media. The thing about auto registration is once you point out the first mark, the software knows at least the neighborhood where it ought to find the rest of them. The immediate vicinity of all registration marks need to be clear of printing but the 3" you reference is overkill.