OK,
Again my addled brain may be failing me, but I thought a section of that line was sold to the State? transportation Group? which set up this Commuter rail system... I'm at work so I don't have my RR Atlas with me, am I wrong about this? and wouldn't whoever bought the section of line be responsible for adding track to it?
Transcon runs east and west, never touch Albuquerque. From the west, it runs along I-40 and then go southeast toward Belen. After Belen, it takes a long and steady climb toward Abo Canyon into middle of nowhere until crossing over Pecos River bridge (Ft. Sumner). The crew stop is in Clovis. Abo Canyon, Pecos River bridge, and BNSF/UP crossing (bridge) are the only areas in NM are in single track. Right now Abo Canyon is in the process of upgrading to double track. Last time I drove was in the spring and they're moving the dirt.
The line that NM bought is Raton subdivision which is not part of BNSF transcon. The line, running north is from Belen, all the way to Colorado, via Albuquerque, south of Santa Fe (Lamy), Las Vegas, Raton, and Trinidad. Few years ago, the frequent traffic was coal mine, but it was closed down. The line is not yet modernized. Some areas are stick rails and most area still used semaphore. If the transcon is congested or shut down due to accidents, BNSF may use Raton subdivision as a relief route, but it is in mountainous areas which requires pushers.
I hope it clears you up.