The specific busyness of these tracks is all the more reason all crossings should be lighted/gated. And while we're at it, there should be sensors/cameras to check for stuck vehicles and communicate that to the train a few miles away - if a train going at 90mph takes 3 miles to stop, that actually means the gates only need to come down two minutes before the train gets to the crossing. But there's no impetus to proactively address such problems until the incentives are reformed.
> I believe it is this circumstance which places the onus on MODOT to defend the users of their later-arriving road from hazards associated with rail traffic on the preexisting BNSF line
Sure, but understanding the legal justification doesn't change what I said. This is an instance where the common law first-come first-serve system completely fails. See also: water "rights". It would be a different story if the tracks were also a public way and open for use by everyone, but in general private control over the commons should be rejected.