No real railroad signal would be that close to the top of a train.

The scene following Gene Wilder first getting thrown off the train was most likely
filmed along the Santa Fe roughly five miles southeast of Mojave. The mountain in
the background looks like Soledad Mountain; at this location, the Santa Fe tracks
point to that mountain. If one looks closely, one can even see the carbon black
plant that used to be on the SP south of Mojave.

It makes sense for the producers of this movie to not go very far from Hollywood
for the desert scenes. The Joshua trees also support the location as being in
the Mojave Desert.

As for the desert ranch scene, I have no idea of the specific location.