>Imagine the expense if every road project had to have an EIR and mitigate the potential impact from more traffic?

Most of the time, they do. However, roads are usually done with public money so the environmental laws all apply to them. RRs have more exemptions, and even with public money if you're just rehabbing in existing r/w the EIR is usually not needed (ask most of the commuter railroads or Amtrak). So what's Novato's angle here? Not clear. But of course if NCRA went ahead and did a EIR and agreed (for political reasons) to do something with Novato they have pretty much given up the ability to assert exemptions so the issue is moot.