Hi, I am not an MTA official but I can tell you this:
Those subway shuttles, are not contained in the GTFS however, they are found in the SIRI feed/BusTime.
HOWEVER, since they do not run on a set schedule, as dispatchers tend to send them out as needed.
The only exception is that if it is a semi-permanent service change (like the A train during the Rockaways shutdown last year), thats the only known time I know those trips are on the GTFS as they will follow a set schedule.
Best way I can think of is do what Apple Maps does, which is somehow predict the routing and use the service change info to get the stops for the shuttle buses, however it may not be accurate, but it is good enough