BNSF is a billion times more cooperative than UP. The delay in restoring the Empire Builder was because otherwise the train would face hours of delay, as happened earlier in the year with previous disruptions.
This is absolutely correct. The decision on when to resume the EB was mostly in Amtrak's hands. Now, BNSF wasn't going to let Amtrak be the first train through, but if they wanted to run the EB through during the first week trackage was back in service, BNSF would not have told them no.
Don't get me started on UP. My post on them would be rejected for excessive profanity.