My understanding is that the Army sent someone out to make offers to purchase equipment, rather than simply comandeering it into government service. I have NOT had the opportunity to go through the relevant War Dept records at the National Archives yet (they're in the 'other' Washington). Some years ago I contacted the Colorado RR Museum and they informed me that the D&RGW management had been quite receptive to helping the Army select equipment for sale to the military.
This may not be as far-fetched as it sounds, since the D&RGW management had been trying to unload narrow gauge rolling stock just before the US entered the war. Sale of a group of passenger cars and two K-27's to the Mexican government in 1940 or 1941 comes to mind.
Since the WP&Y was coal fired, I suppose the Army decided that it wouldn't pay to pick up the Pacific Coast locos (some went to Hawaii), but the K-28's and the three remaining SN locos were available, and could all be had without too much protest. The SN was effectively dead, and the D&RGW had a lot of stored motive power on a narrow gauge system it was trying to kill off.
My question has always been- Why didn't the White Pass pick up the three SV Baldwin 2-8-2's along with the two ALCOs? Perhaps the Peruvians offered more $$?
Charlie