Stainless steel isn't that hard to paint; just think of all the Budd-built stainless steel cars that were manufactured in the mid to late 1950's and were delivered painted. Think NP, UP to say the least. Cars were delivered fully painted. As for the tan color over Cajon, keep in mind just for giggles that many of the signals on the run between Mojave and Barstool were, and most still are, I think, painted tan. But I believe that had more to do with visibility than asthetics.
Part of BNSF's Mission Statement, or other similar policy, reads, in part: "...strive to be a good neighbor to our communities..." Given that the company, in the years 2005-9 will succeed in putting an enitirely new main track through such an area AND in this cultural climate of environmental concerns, as well as other political issues, painting the signals tan would seem a small concession.