I think the some of the marathon series are sized bigger then one would expect. My Marthon XRs 35s are big and really closer to 37s I'd say. Schwalbe's website lists my tire's ETRTO # as 37-622. Your plus's have the same ETRTO number.

Does seem odd that xrtracycle doesn't allow more room for 700 tires and fenders. My bet is that they designed it with expectation that more people would attach to mountain bikes with 26" wheels which should leave loads of room for tires and fenders.