My recollection from the last time I spoke with someone in the legal profession (Joe Wenninger of the Crowe Law firm) about whistleblower suits is that the whistle-blower laws applied to Guvmint employees and not really a private company's workforce. This meant that a case could be made if said engineer was employed by Amtrak because even though a "corporation" it is a Government corporation which receives all its funding from Congress and the Government appoints 100% of the corporate directors. The Supreme Court has already ruled (1995) that because of this, Amtrak is bound by the 1st Amendment. The BuNSifF is a private corporation, so it isn't bound by such strictures. If, however, a private company receives Govmint money in the form or some sort of subsidy, then it begins to be emmeshed in these types of legal constrains. Being paid by some governmental authority to run its trains on the BNSF's tracks doesn't really qualify as a subsidy.

It's quite possible the whistleblower laws have been strengthen to cover private companies -it's been at least 10 years since I discussed WB laws with Joe- but I don't know whether this is the case. Also keep in mind that on the RR, State and Local laws are pre-empted by Federal law (the RRs want it this way).