Methinks the STC and move from primary category are because that's the only way to do it within the existing paper-blizzard infrastructure at the FAA.
It is true that the airplane is reclassified to primary category - I think that's so it fits into that line-item in appendix 'A' that mentions primary category. Any subsequent airplane would also be moved into that category before the owner could work on it. Moving it back is easy according to Rick Hestilow.
