Don't know the answer to this, although I have an idea, but in hopes of prompting someone who does know I'll mention the following.
I have the original VL (2009) version of this and I don't think it has sounds for all the place names you mention. In videos of the more recent version, the sounds consistently reference Albuquerque, but I think it would be pretty unusual for a Lionel model to reference more than three place names in the tower sounds/crewtalk announcements.
Ignoring for present purposes other people's objections to having these announcements at all, I'm also not sure what might be regarded as arguably historically accurate. I understand that there was a Santa Fe depot in Flagstaff from 1889 but it was rebuilt in 1926. These particular engines only operated for a short period of time between those dates starting from 1911, and I thought they were mainly used on routes further west.
I hope to be proved wrong. Anyway it's a great engine.