You may be better off using a same size box system but there is no must - that is just as blinkered as saying you must use a QX full stop many misguided people work brood and a half - that gives the same 'logistical problem' of two sizes od brood frame, but they cope.
Same goes for the statement of you must keep the brood out of the honey boxes it's not true, just because most of us choose not to leave the queen a free rein, doesn't mean we must not.
The different sized boxes (i.e. using shallows over deeps) is just for the convenience of lifting slightly lighter boxes come harvest time, it doesn't mean that the bees are not allowed to brood in them the rest of the time.