These bridges certainly were built as part of the cutoff project. Having the railroad run the project probably cuts a few corners, but not many; Caltrain is still a public agency. The pictures in the presentation slides make the need pretty obvious - old steel plate girder bridges that need work generally, for seismic safety reasons, and because cars and trucks are just bigger and heavier now.
That said, look at slide 7 at [
www.caltrain.com]
Paid for by Caltrans (most likely Your Gas Taxes at work); owned by the City; maintained (and this is unusual for grade separations) by Caltrain.
Disney Construction Inc. - naw, couldn't be the same family, could it?