If you have a U-type structure with microstrip ports coming in next to each other, then you should try to terminate them at the same reference plane. In that case, regardless of how close or far apart they are, there will be a "grouped calibration" which will eliminate any port coupling between them.
Otherwise, you may find that using internal ports is actually more accurate if the ports are very close but not on the same reference plane.
Otherwise, you may find that using internal ports is actually more accurate if the ports are very close but not on the same reference plane.