If it terminates as a "station outlet," then I would ask the engineer to reference the code supporting his exception.
NFPA 99, 2012 explicitly defines instrument air as a medical support gas.
3.3.84 Instrument Air. For the purposes of this code, instrument air is air intended for the powering of medical devices unrelated to human respiration (e.g., surgical tools, ceiling arms). Medical air and instrument air are distinct systems for mutually exclusive applications. Instrument air is a medical support gas that falls under the general requirements for medical gases.
Furthermore, NFPA 99, 2012 is explicit that the requirements apply to all medical gases and medical support gases.
5.1.1.2* Where the terms medical gas or medical support gas occur, the provisions shall apply to all piped systems for oxygen, nitrous oxide, medical air, carbon dioxide, helium, nitrogen, instrument air, and mixtures thereof. Wherever the name of a specific gas service occurs, the provision shall apply only to that gas.
So, the use point in question would require a zone valve compliant with 5.1.4.8 through 5.1.4.8.8:
5.1.4.8 Zone Valves. All station outlets/inlets shall be supplied through a zone valve as follows: