The pipeline crosses several states (Interstate Commerce); more than likely crosses over federal land and it crosses an international border so there are several items which involve the federal government and thus, they have the power to grant or deny.
I get that, still, there must be some protection for the contractors in their contract clauses, otherwise no one would ever do business with the govt. I see this in the defense industry all the time. The contractors aren’t stupid. Unlike our fickle government...