Yes, the Sprinters are under a waiver - time separation. Freight equipment cannot be on the line at the same time as the passenger vehicles, which *are* diesel-powered light rail (US-adapted, but not FRA-compliant, Desiro model). So they operate as a transit line under CPUC and FTA regulation. There isn't much freight traffic on the branch any more, but there is some, and it runs in the middle of the night.

In 2013, all service was shut (bustituted) down for a while due to brake issues (see, for instance: [www.utsandiego.com] - many more details can be found chez Google). During the shutdown, freight trains appeared during the day. May have surprised a few people who didn't know freight still moved there. 'Twas reported here too, of course.

I'm pretty sure SMART is different - more like the Westside line in Portland or the Dallas RDC lines - because there's no separation from freight traffic. So it falls under FRA jurisdiction. That presumably is where the conductor requirement comes from.