I'm pretty sure there are better ways to get to Back Bay from Downtown Crossing than to get on the Commuter Rail. And don't get too excited about Itinerary 2 -- it's just the Needham train instead of the Providence train.
And no, I didn't type "downtown crossing, MA" -- I typed "downtown crossing" and it added the ",MA" of its own accord. Strangely if you choose Downtown Crossing from the list of stations instead of typing it in manually, it works correctly and suggests the B line. Or if you include the word "station".