I believe that the portion of the pipeline that goes under the Missouri River is a wide spot (”lake”) created by a dam, and the area is owned by the Feds and run by the Corp. I read where the pipeline company started construction of the line (85% done now) without the final permit for this section, but must have figured in talks that it would be a done deal. The company also said that it already has the mineral rights to this land, and that they will use those rights to allow them to bore under the lake.
I thought they just won a court case and that is why they are working. In fact, people mocked Obama for saying, just a couple of months ago, that maybe a new route could be chosen. And it was because the court ruling was the final say.