Every flight, every day, by the military is on a flight plan.
Even those flights on VFR MTRs?
Yes.

Does ATC track those flights in real time, at least with non-radar
position reporting? If so, then ATC should be able to provide better
information that a civilian pilot could use to determine whether or not
to transition a route at a particular point at a particular time.

Jose
--
The monkey turns the crank and thinks he's making the music.
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