Third, what I'm referring to are laws that are already in effect. For example Federal laws stipulate that boats get priority over trains; and trains get priority over cars, trucks, and pedestrians. Therefore if some town in say California for example suddenly passed a law that said trains had to stop at the one crossing in town whenever a car was approaching, that law would be stuck down by the Federal courts and any fines imposed upon a RR for violating that law would be thrown out.
I imagine this falls under the Interstate Commerce Clause of the constitution, which is the most vague of those vague clauses that you mention in Constitution (recently used, as you recall, unsuccesfully to try to extend Endangered Species Act protection some kind desert toad in the Southwest). Judging by PRR's posts, it is not interpreted or, at least, the Federal Government has not tried to interpret it to allow the Federal Government to deny states the right to eminent demain on railroad property -- at least certainly not if that right was being exercised on, say, an abadoned right-of-way or merely to install a grade crossing which would not significantly inhibit (interstate) rail traffic on the line. Anyway, this all sounds like quite the mess - I'll be quiet until one of our lawyers has a look!
PRR, did you like the job at the PUC - it sounds interesting.