In Caltrain's case, they actually got an interesting waiver that allows them to time-segregate the network, where it's part of the national rail network (and can accept freight traffic) at night, but cut off from it (with no freight traffic, and interlocks making sure it's disconnected) during the daytime. In that setup, it would have permission to run non-FRA passenger-rail equipment: http://wilshirevermont.com/2010/05/31/caltrains-amazing-waiv...

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.