Hi! I worked @ BART for over 26 years. YES, there is ONE connection to the National Railway Network. It is located at Hayward Yard, and it has NEVER been used. Way back when the system was still being built, the original idea was that the original BART passenger cars would be delivered using the connection. The trucks would be standard gauge trucks for the journey from ROHR in San Diego, and the undercar equipment would be installed along with BART gauge motorized trucks at the Hayward Yard. The cars in transport would be hooked to a consist of regular railcars while in transit from San Diego. NEVER happened for reasons I don't know.
When the time came to deliver - was all done by TRUCK, each car was configured as a trailer, along with the BART trucks (wheels) and pulled by a rig from San Diego up I-5, every BART car was done this way; and all cars purchased later - C1, C2, as well as the rebuilds -A1, A2 - were done the same way. The Bombardier cars will be delivered by truck as well.
I am not sure if the connection is still visible on the road after the parking lots by Hayward Yard,as it may be paved over now, but looking through the gate you can see an "extra rail on the inside of the track nearest the fence by the front entrance which would have been the track set used for delivery. Of course once the car would have been detrucked and rechecked Bart gauge, that spur was irrelevant to all moves in/out of the shop and it still is!!