I can confirm the public is welcome to ride the free employee shuttle. I've done a dozen or so roundtrips.

The only pick-up/drop-off point at SFO is the INTL terminal, the curb directly outside the airport BART station doors. Look for the "employee shuttle" sign.

The pick-up/drop-off point at Millbrae Caltrain/BART station is the bus plaza on the east side of the station, south of the parking structure. After exiting the trains, go up to the 2nd level and take the elevator/escalator down. As a point of reference, you will be able to see In-n-Out from there.

It's a direct, non-stop bus which takes approx 7 mins one way, so you could expect the bus to circuit every 15 mins.