BNSF are friendly to railfans and apparently quite willing to work with LEGO, as this is their third joint project. The new loco is in their modern colors, dark green and orange with yellow striping. The 10020 loco is in the passenger colors of their predecessor line ATSF (BNSF is a merger road from Burlington Northern (BN) and Atchison Topeka and Santa Fe (ATSF))
Union Pacific have a reputation among other railroaders as the most arrogant railway in the US. That reputation extends to model railroaders as well, as they are rumored to have sued model companies for using their logo (within their rights) after wanting exorbitant license fees, fees that would break a mom and pop operation (also within their rights). Their color scheme is yellow with red stripe and gray trim, not "all yellow"
So it may be that LEGO either chose not to work with UP (I could tell a story here about a conversation Brad and I had about who was easy to work with and who wasn't, well before the 10020 came out, but I won't... who would believe me?), or UP blew LEGO off, or wanted exorbitant fees.
Despite that, UP is the most popular color scheme for my MTW-2001 loco. It IS a sharp scheme.
Hope that helps. I admit bias. BNSF is a customer of my employer while UP is not.