Let me ask a new question...
If BNSF did not want Amtrak on this portion of the transcon, do they have to let them on? Or can they go the UP route and say they have to pay a bunch of money to upgrade the lines if they want to use them?
If they do not have to, then that would mean the whole route would be at risk.
My understanding of things is that they only reason that BNSF is allowed to let maintenance go on the current route is because they are offering to accommodate Amtrak on the Transcon. If BNSF were to withdraw the offer, then they would have to pay for the upkeep on the current line.
Now if Amtrak was requesting either to change the current routing on their own, or if they wanted a new service that used the Transcon, then that would be a horse of a different color and BNSF could demand major bucks for improvements. BNSF couldn't however out and out refuse either, as then the FRA would step in and order the change. This is why UP didn't say no to Amtrak's request for a daily Sunset. Instead they set a ridiculous price tag.
If Amtrak decides to pursue things further to force UP to agree, the odds favor that UP will still get a decent chunk of money to allow Amtrak to make the change. They won't get what they're asking for, but it wouldn't surprise me that the settlement gets close to half of what they're asking.