I flew the following itinerary earlier this year:
YVR-YYC (AC)
YYC-DEN (UA)
014 ticket, Z fare, but YVR-YYC was seated in Y (showed Y fare class on the ticket receipt from Amex Travel). The AC flight credited as 'T', which every AC flight seated in Y since the advent of branded fares has credited as for me regardless of booked fare class. Like every other AC flight I take, I had to write into MileagePlus to adjust the earnings to the correct amount for the booked fare class (Y).
So uh, not sure that really helps but suffice to say flights don't appear to be credited based on fare basis.