The Knights have quasi-diplomatic status; in that realm, they claim to be "Sovereign."  But they also have the characteristics of a religious order; in that arena, do you think their 'sovereignty' trumps that of the Sovereign Pontiff? Some members, including the leadership, make the traditional vows of poverty, chastity and obedience; others make simple promises. As a Catholic order, they surely recognize the authority of the pope and will defer to him.  Or maybe they won't.  If they don't, they can sever the relationship with the church.  That may not make much difference to them. They can certainly carry on the trappings of a military order without the ancillary trapping of a religious order.
Obviously the American Sisters are better religious than the Knights are, and take their religious vows more seriously than the Knight do; but then the Sisters aren't trying to do double duty as a medieval military order.