If you look closely at these flights, you will see that the 9:20AM departure and 11:30AM return flights do have Saver fares at $129 one-way and Main(R) fares are $157. The other 3 daily flights do not have any Saver fares and just have $127 Main(R) fares. This is undoubtedly due to B6 who is likely the fare setter on this route and does not yet have Basic Economy fares. There's no B6 flight around 9:20AM, so AS seems to feel they can charge a premium for that particular flight. There is an 11:10AM B6 JFK-SFO flight, but that time slot likely has sufficient demand that AS feels than can compete against B6 with pricier Main fares.
But those flights do have a saver fare at $129. You can't see it on the Alaska website (I think they hide saver fares when they are more than main) but they show up on matrix of you limit to f bc=x. So there is a published fare that books into X and there is X space... it's just more than the R fare.
In other words, both main and saver exist; the "buy-up" is just negative.
That seems strange to me. I'd think that if they didn't want basic economy on some flights, they would just zero out X space on those flights.
On any case, maybe it's intentional and maybe not, but it's nice to see 2018 pricing for main reappear for a major route.