Paper asked:
Do we want to match the size of the captain chainring (sync/timing) and the stoker chainring (sync/timing)?

Veggie, unless I misunderstand Paper's question, the captain and stoker chainring (sync/timing) must match, or else they will be WAY out of sync most of the time. This will lead to having difficulty with some turns, as the Captain has no way of knowing or changing the position of the stokers pedals when encountering a corner. Even having the Captain and Stoker OOP (out of phase) is okay as long as the Captain knows where the stoker's pedals are, but with differing size chainrings, he will always be guessing - or have to communicate this with the stoker while trying to negotiate turns.
Leave the sync/timing chains the same size whether staying In Phase or Out Of Phase.