Caltrans was appointed to study the extension to have that separate ROW as endorsed by SP interests in order to dump the Penninsula Commute Service long before Caltrain was concieved.

Caltrans did not select the first corridor proposals to keep the San Diegan, the San Joaquin Daylight and the Coast Daylight as Railpax statutes show could only find Long Distance services.

So, BART D was formed under the MTC umbrella kept separate from the Espee, BUT still: Caltrans thru State of California's agenda pushed to keep the Peninsula commute. The rest being history.

However, it looks like BART was given the East Bay with funding from AC TRANSIT too! Somewhere over time, the BART from SF to San Jose project was eliminated, but I used to have a map of where it was going to go thru. Not a bad idea for the future, providing "excess capacity" for the service.

My 2 cents