It isn't mind blowing to think that Rosenstein might have appointed Mueller into a somewhat protected (i.e., independent) position to provide him a modicum of cover (i.e., a shield of sorts) from claims of U1 or other improprieties.
Which makes me wonder what actually was said when Mueller went to the White House. I believe Trump has been aware of all of this and is letting it play out as he has the drop on all of the players.
Mueller, Rosenstein and even Sessions are all protected. All three, if fired, would trigger an obstruction charge and an impeach cry, from the media and from many in Congress. Thus, for now, they still have their jobs.
And all three, while they still have their jobs, prevent the Deep State, including themselves, from being prosecuted. They are the prosecutors.
It's quite gambit they've set up.