I have never seen a smoking gun. As I have posted before, there are direct links between Bechtel as a member of the managing consortium PBTB which made technical decisions and Espee. S D Bechtel Sr was Chair of the SP (holding co) and S D Jr was a director. What we have is circumstantial evidence of potential influence. Since no one involved in those technical decisions (to my knowledge) has ever written or spoken about about it, we don't have direct evidence.
We do know that Espee did want out of what today is Caltrain. We do know that Espee behaved so agressively in trying to get out of all passenger operations that the ICC forced them to restore on board services. As with any history where the records aren't available, one has the choice of infering a likely scenario or not.
Mike Healy, both in an interview w/me decades ago, and in his recently published memoir, makes the case for better stability in the high wind conditions of the Bay Area. I would notethis is irrelevant to the subway segments). At the time the decision was made, CTA held the rappid transit speed record--achieved in the Windy City with PCC based L cars.

Your mileage may vary.

All that said, we have BART, I use it regularly, and we are NOT going to reguage it. The US has multiple examples of non compatible rail segments--the former PRR and NYC owned/operated commuter lines around NYC use different third rail systems. These are the legacy of intense corporate enmity from which the public has not benefitted.