I don't think you should worry too much if the mcc is the only item that has been taken off the menu. The main thing with an integrated ATPL or CPL/IR is the training route "ab-initio" - you don't have to get a PPL issued, the training is integrated from the start so you do your flying and theory moving you towards the CPL and then ME/IR, all with the same training provider. Where you do your MCC course really won't matter too much, so long as it is a reputable provider, but you do need this for the fATPL.