Ethan,
I don't have any additional context on the MTA feeds and OBA, but FWIW OpenTripPlanner supports an interpretation of GTFS-Realtime ADDED trips:
I don't know the exact behavior but I believe it's used in the Netherlands deployment. In theory I believe you could pass through #3 "novel trips" into OTP using this if you had a converter in between the MBTA feed and OTP.
Thinking more about this, the MTA subway feed (which I don't have any experience with) sounds more like a true frequency-based feed (exact_times=0 trips) in principle. See some discussion at
https://groups.google.com/g/gtfs-realtime/c/ujeIp2UTnCs/m/DmhpatE-FQAJ for how these work in GTFS Realtime. tl;dr - real-time trips are materialized on-the-fly from the real-time feed and anything that's not in the real-time feed doesn't exist (i.e., there is no "scheduled" service), which sounds a lot like your description above.
OTP2 has work-in-progress support for true frequency-based trips, although I'm not sure if it includes real-time support:
OTP1 supported static data for frequency-based (exact_times=0) trips, but not real-time data.
Sean
Sean Barbeau
Center for Urban Transportation Research
University of South Florida