Based on my luck that my watchful waiting for my NYP-EVR trip turned out, now booked, with fares inventory being allocated from all high bucket to lowest bucket on the Lake Shore and second lowest on the Builder, I did a check on days in October that the Zephyr arrives in Emeryville one day before the Sunset/Eagle leaves LAX. It appears that some inventory reallocation has taken place, because the fares vary quite a bit now:
10/2 high bucket
10/4 high bucket
10/6 second highest bucket
10/9 high bucket
10/11 middle bucket
10/13 middle bucket
10/16 middle bucket
10/18 middle bucket
10/20 second lowest bucket
10/23 second lowest bucket
10/25 second lowest bucket
10/27 second lowest bucket
10/30 low bucket
To me, that indicates at least a first round of inventory distribution adjustment has taken place. Only 3 of 13 departures are now high bucket.
I don't know your planned itinerary, but October and November now appear to have been reallocated and it is the time to strike if any of the middle or second lowest bucket dates appeal to you. They typically only have a couple of rooms in the lowest allocated bucket, and I would never hold out waiting for a low bucket when a second lowest is available. Of course, you could score on 10/30.
That kind of search is what is needed to track down good fares. Amsnag made such searches easy, now they have to be done by hand. It isn't worth doing until there is a good chance that they've done an inventory adjustment after the initial allocation, spot checks are good enough in the first few months.