Grant seemed more aware than most about civilian control of the military.
An understatement of the first water.
Grant was all about subordination and civilian authority. It's part of what endeared him to Lincoln and a big reason why he rose high. Unlike a McClellan or a Hooker or most anyone else he didn't second guess the administration, or if he did he kept it to himself. An order was an order, end.of story.
He also expected the same from his subordinates, which is why in turn he loved Sherman so much. Not that Sherman didn't have a big mouth and a lot of opinions, but when Grant ordered something it happened.
One of my favorite Western war tales is right after Grant headed west after taking Jackson Miss. He left Sherman to wreck the place but then discovered he was about to run into Pendleton at Champion Hill.
So he sent back word to Sherman that he wanted a division and an ammunition train sent to him, and literally within the hour a full division as on the road, followed closely by a mountain of ammo. As Grant knew it would be.
I've always laughed that the Army if the Potomac couldn't have pulled it off in much less than a week. There would have been a list of objections and problems and delays and shortages and excuses.
Grant expected prompt unquestioning obedience from his people and he gave it to those above him. It's a key insight to understanding the man.
As.for the overland vs. Waterborne approach Grant was probably right that the James was his best route but that had been the McClellan route and that was such a disaster that no one in Washington was going to approve a repeat.
By that point anything that smacked of Little Mac was anathema to the administration.