The floor at Alamosa was definately concrete, as is the floor in Cheyenne. The concrete floors I have seen have the rail just above the top of the concrete--you don't want the weight of the locomotive bearing on the edge of the slab! Usually, the rail sits on chairs on the pit walls.
Wood is not as flammable as you might think. Large columns perform well in fires, with the fire only getting at the corners where there is lots of oxygen--hence the chamfers you see in lots of large timber warehouses and roundhouses.
Wood has great compressive strength, so wood floors with the wood on end so that the radial grain is exposed is a popular floor for uses with heavy loads--machine shops for example. These floors today tend to be quite expensive.
On the narrow gauge, it seems most all of the service facilities had dirt floors from photos I have seen-Ridgeway, Gunnison Car Shop, the Silverton Engine Houses, Rico: Mike Trent might comment on Como.... I guess the dirt just soaks up the oil and crud better! There, the ties just sit on top of the dirt, or on top of the concrete pit walls if there is one. Earl or El Coke probably have a better memory of the condition at Chama.
Considering the rather large weights of locomotives and the point loads imposed on jacks, I continue to be impressed that railroad builders could lay track on just about anything, and build big shop facilities in river bottoms. Today, the geotechnical engineer would call for elaborate excavation down many feet and importing structural fill to be compacted in 6" lifts. Has anyone tried to dig a hole in the Chama floor?
Keith