If Caltrain did a symbolic disconnect, cut off several feet from the track, put up a barrier, a few days work to do and undo. from the national rail network, would they still be subject to the FRA?
However I believe implementation of this is on hold, because they want to coordinate any upgrades with the HSR project.
They've also discussed completely cutting it off from the national rail network at times. Unlike in many places, Caltrain actually owns the rails (rather than a freight network owning them), so that would be possible. There's strong lobbying against it from various landowners along the line, though; even though the line doesn't get a lot of freight usage, the possibility to receive at least an occasional freight shipment increases the value of the land.
Caltrain has so far, however, refused to go down that route. Apparently the one freight train per day is too much to lose.