The old novel Enterprise: The First Adventure
by Vonda McIntyre had Admiral Noguchi running Starfleet in 2264. I always thought Noguchi was meant to be Nogura (from TMP) - the novels were prone to some incomprehensible last-minute changes back then.
But of course the novels aren't canon. This one came up with the names of Kirk's parents used in STXI, but in the book, during the ceremony where Kirk is given command of the Enterprise, George Kirk is said to have vanished mysteriously on a mission years before - wheras in the movie Spock Prime says he was there.
So... I guess you're right. Marcus could
have commanded Starfleet at the same time in the Primeline too.