The fact is that it is Kelly, and not the president, who is the decider in the Trump White House. Yes, the president can fire Kelly. And yes, the broad policy agenda of the administration is largely a function of the priorities Trump set during his presidential campaign (which Kelly shows every sign of endorsing). But beyond that, it’s hard to imagine a situation in which Kelly would not be able to shape, and even to get away with actively overruling, the president’s decisions.
He’s already done so, in broad daylight, on multiple occasions — most recently and most dramatically on immigration, when Senate Minority Leader Chuck Schumer (D-N.Y.) believed he had reached a compromise on immigration in conversations with the president only to learn from Kelly later that same night that the terms of the deal were unacceptable. Kelly has also publicly countermanded the president on the border wall, North Korea, and other matters. How many times has he avoided the need for such public corrections of the commander in chief by manipulating information the president sees so as to avoid him taking supposedly unacceptable positions in the first place? That’s something we might not know until Trump leaves office, if ever.