John,
From 1982 to 1992, when I left the D&S, I never heard of any problems or comments by FRA inspectors regarding the "dual" brake system as applied on the D&S equipment. This may have changed since then, but I don't know.
Regarding interchangability, the "straight air" equipment as installed on the D&S equipment is completely stand-alone and separate from the original automatic air equipment. The two systems converge at the exhaust port of the K triple valve on each car. Thus, for example, a coach from Durango could be loaded on a truck, transported to Chama, and coupled into the train there with the automatic air system and would function just like all the other C&TS coaches. The only difference would be that the straight air line would not be connected. Likewise, any D&S locomotive could be operated on the C&TS with no modification--the straight air equipment in the cab would simply remain idle and unused. C&TS coaches could operate on the D&S, but doing so would preclude the use of the straight air system on the rest of the train.
Applying the "straight air" system as used on the D&S equipment to more modern equipment such as A-B systems or others using dual auxliary reservoirs might not be possible, and would probably not be necessary, as the equipment already has built-in redundancy.
The fact is, the usefulness of the straight air system as used on the D&S, is probably very limited in other applications. The brakes are slow to apply, as the air from the straight air line must pass through a relatively small exhaust port in the triple valve to get into the brake cylinder. This would probably make train handling over undulating territory somewhat difficult. Also, as described before, any trains over approximately 30 cars in length would be difficult to handle because of delayed application and release of the brakes on the rear cars in the train. Where the system is ideal is on long, unrelenting grades (miles of 2%+) on trains using antiquated K-type triple valves, where there is a danger of depleting the air in the auxiliary reservoirs from constant cycling of the automatic air brakes. The D&S and C&TS are about the only two roads I know of where the dual system would be effective.