I disagree that the two maintenance facilities are expensive or foolish.
Caltrain's facility includes an operations building, wash, and storage tracks, as well as the actual maintenance bays. It is designed for Caltrain's fleet of commuter cars and engines. Except for operations, these are new functions for Caltrain, which was sending engines and cars to facilities in Los Angeles and Oakland (among other places).
Amtrak's facility has a main shop, wash, and a service and inspection area. It is designed to maintain Amtrak California's fleet of engines and cars; and service trains using these cars, as well as Amtrak's long-distance trains. This replaced an older facility in Oakland.
Considering the space constraints in San Jose, their intended purposes, and the distance and tracks between the two, I don't see how Caltrain and Amtrak could share a facility.