1234,
Yep. The airplane is Certified and equipped for 50 passengers. Then the operator calls up and says, "I need a certificate for 44 passengers to meet a scope clause." Since the requested operation is less than the real capacity the manufacturer says, "stand by one." They print up a TCDS for a 44 passenger CRJ200, call their FAA program manager and throw the thing in the fax. In effect, weight is simply removed (as long as the result is within Certified CG limits) and the airplane performs a little better with a big closet where 3 rows of seats were. Or, the seats are not sold, resulting in a semi permanent operation at 88% of Certified capacity.
Delta's MD88's are Certified for higher weights than Delta operates them. Republic's E175's operate under different weight limits for different airlines. It is common industry practice.
Literally the airline's mechanics can come out and put a few stickers on the airplane, put in the logbook that it now conforms with xxxxxxx and off they go.
It is one reason why ALPA's scope restrictions are not really that restricting.