NHRA is trying to bring back the rivalry between the manufacturers in Stock and Super Stock.
They're also trying to be flexible regarding engine/body combinations to allow the Drag Pak (and Cobra Jet Mustangs) to run various classes.
This why there is a 5.9L Magnum listed in the classification guide for the Challenger and also a 428 and 352 (both based on Ford Racing's 351W platform) for the CJ Mustangs.