To be sure, you would probably have to ask BART - as if they would talk about such a probably not-yet-fully-negotiated HR item. But since e-BART runs only in the median of the freeway, and apparently has no connection with the "general railroad system," it would probably operate like any other transit line. It might have been different had it run on UP.

Track gauge isn't the issue with railroad rules applying: connection to the railroad system is. Lots of transit lines are standard gauge and don't have FRA involvement; certain people who frequent this board argue that BART itself should have been standard gauge - a useless argument at this point.