I think you completely misunderstood the article. It says that the electricity used to power these trains was estimated to cost $19m a year, but the trains are a bit more efficient than expected, so the new estimate is only $16.5m/year.

Most if not all electric trains powered by overhead wires have regenerative braking that feeds back to the grid as standard, and Caltrain's new Stadler units definitely do. Nobody paid extra for regenerative braking, it's just the default way to do things on electric trains, to the point that it'd be weird not to have it. Even diesel-electrics often have a kind of regenerative braking, but they don't have anywhere to store the recovered energy so they just convert it to heat via huge resistors.