Delta has, or will have, competition on nonstop JFK/EWR - SFO/LAX/SEA routes from AA, UA, and B6, not to mention those 4 cities have lots of mutual origin/destination traffic. Given the preception (or perhaps actuality) of there being "enough" people in those markets to pay for a premium product, Delta is going to try to capture that market. Also, there are multiple flights per day from NY to each of the west coast cities.

ATL has few, if any, of these factors. There is a single AS nonstop ATL-SEA per day, and a twice-daily UA ATL-SFO nonstop. While there is O/D traffic from ATL to the west coast, it's not of the same size or profit margin that that of JFK/EWR is. Basically Delta is the only game in town, and for better or for worse, doesn't have to fly a premium J product and service on those routes.

As a side note, what exactly is the definition of a transcon flight? To me, anything that is a nonstop flight from the Pacific time zone to the Eastern time zone (or vice versa) is a transcon, but that leaves some questions about cities that are closer to the time zone boundaries (LAS in Pacific; DTW, CVG, IND in Eastern).