Part of modular schools' recommendation system to flybe is based upon doing the PPL, Night, CPL, Multi & IR at the same school, the MCC is irrelevant, it can be a tick in the box, but it can also be more, for instance, my sim check with an airline was done in the exact sim I did my MCC in, did it help the sim check? of course it did. You just have to be a bit smart about it.
But back to the question in hand, for the application form I would imagine they are only interested in your "commercial" training being 1 stop modular, excluding MCC of course.