Cross Country (XC) are only allowed to use platform 2 at Stansted Airport, which is only 106m long. Platforms 1 & 3 are 359 and 291m respectively, but are needed for the Stansted Express, which regularly loads to 12 x 20m vehicles. The only trains XC possess which are (a) available and (b) short enough are the 2 and 3 car class 170 DMUs.
Regarding the penchant for Northern to run 2 car trains in the peak and 4 car trains off peak, at the moment they are required (in the franchise agreement) to run extra trains during the peak, but until the new/second-hand fleet are available, they don't have any extra trains (also in the franchise agreement!) to run those extra services. Guess where the extra trains have to come from...
(This used to happen all the time on the Leeds - Harrogate - York line where 2 x 2 car trains off peak were split to provide extra trains for the peak. Then they got some 3 car trains from Scotland - longer vehicles and 2 fewer cabs and vestibules to worry about = roughly the same number of seats. To quote a guard "At least they won't be able to split *these* buggers in the peak!!")