You're right that the environmental exemption should apply, as long as all the work is within the existing r/w. But Metrolink (they seem to be the railroad branch of MTA, though I'm sure it's more complicated than that), being publicly owned, is subject to politics and in this case seems to have yielded to that; once that happens, they may choose to do the environmental studies even if they don't actually have to. It might be a balancing act (studies vs. lawsuits) but it doesn't help as a precedent. Several other publicly-owned railroads (San Diego a local example) have made better use of the exemption.