I can't say precisely how they're doing it, but SacRT does have crossing gates/signals tied into its block signal system on PRW (and street running in some spots). It appears to have been retrofitted in areas that don't have actual signaling.

RT doesn't actually have block signaling for train control; it's mainly for controlling train movement based on crossing gate closure. That's been one of their excuses for not running expresses or limited - they would have to add more blocks, signals, and control systems. I think they could do a limited-stop train without changing much, but I'm not the Boss, just an occasional rider.

In action, when a train clears a grade crossing, the gates clear immediately - no significant delay - unless another train in the other direction has triggered the gates. In places where some distance between stations, with several grade crossings, the grade crossings will generally close in a timed progression based on track speed, so only the first couple of gates will actually close before the train is allowed out of the station on a yellow. If the train dwells in a station long enough for ALL the crossing gates between there and the next station to close, it'll be cleared with a green. Just outside of the downtown area, there are places without "block" signals but with crossing gates; at stations in those areas, an auxiliary signal is attached to the wheelchair loading platform within view of the driver, indicating either stop (horizontal bar) or proceed (diagonal bar) - proceed appears when all of the gates between there and the next station are down. At least in signaled territory, there does appear to be some form of ATS and speed control system - running a red stops the train in emergency, and passing a yellow too fast will also trigger braking though it seems like the driver can override that after reducing to restricted speed. I understand (from a presentation seen many years ago) that the trains and wayside equipment have some kind of radio communication so the system more or less runs autonomously - Central/Dispatch mainly observes and deals with anomalies and reporting (login, logout, location, passenger issues, etc.).

Considering that SacRT was initially built in the 1980s, and other than extensions and some new cars hasn't seen many changes since, I wouldn't be surprised to see similar control systems on other light rail lines that don't have very frequent service. RT's minimum headway is 15 minutes, outside of downtown where VFR is in effect with some extra heads on traffic signals to govern trains, and maximum speed is 55mph on PRW sections in the 'burbs. Lines with less service or lower speeds probably operate more on a streetcar model (VFR with perhaps some traffic signal augmentation).

Oh yes, a couple of lines share r/w with freight rail. The freight line operates on its own tracks with its own track circuits, tied into the crossing gates also used by RT. At no point on their system (now that the dirty dirt track crossing on 7th St. is gone) does RT actually connect with the freight rail system. Not much problem along the Gold Line on Folsom Blvd, since the freight line is an industrial lead with low-speed activity maybe 3 times a week. The Blue Line follows the UP Sacramento Sub (old WP line) on which there's considerably more activity.

Yes, when you're in a car or on a bike or a pedestrian waiting for a crossing gate, along the Blue Line especially, Murphy Lives - inevitably, when a freight train goes through, light rail will appear just after it clears; sometimes the other way too. Part of life if you travel through that area, relax!