Talk of extending the RailRunner to Las Cruces is just that: talk. There was enough of a stink over how Bill Richardson handled the funding and construction/rebuilding of the ABQ-Santa Fe route (when he wasn't off playing ambassador-at-large) and it's not too likely extending service further south will happen without a lot of funding from Washington (good luck on that!!). Throw in the need to rebuild the entire line from Belen to Las Cruces (which would likely cost as much as rebuilding the Raton Pass route) and the simple fact that any trains to or from Las Cruces will have to run through the BNSF yard at Belen (or else use a bypass route that would require buying - or condemning - property whose owners aren't likely to sell for whatever the state offers) and it's not too likely that there would be enough support in Santa Fe to move forward with the idea.

I should point out as well that those semaphores will have to go anyway as part of upgrading the line to CTC/PTC, which would be a requirement if the current route is somehow maintained. Also, it's not very likely that Amtrak will find a suitable location in or near Belen for a new passenger station with refueling and crew change facilities (or at least one that BNSF would approve of, even if it is pushing for rerouting the SW Chief), which means that Albuquerque may be retained as a stop anyway. There is a wye which straddles the intermodal facility south of the main BNSF yard in ABQ which trains 3 & 4 could use, although it does need to be rebuilt (that's an easy fix, though).

(Personally, I would much prefer keeping the current route; I'm also a realist, though, and I don't believe that's gonna happen unless Washington coughs up the money needed to make it happen, which doesn't seem very likely right now. I'd love to be proven wrong, though...)