
Religious orders don't have bishops as their superiors. Any of them, as far as I know. In fact, when one of its members becomes a bishop, he is no longer a part of the order, since his rank is greater than the order's superior.
They merely work together with the bishop of the dioceses on which their houses are located. It's not like the bishops interfere with their affairs.
If I understand correctly, congregations of "pontifical rights" answer to their superior and then to the Pope alone, merely colaborating with diocesan bishops. If a congregation is of "diocesan rights", their answer to the bishop instead of the Pope.
Groups like the Dominicans have had "pontifical rights" for centuries. In regular times, they had only the Pope above their superior general (or whatever title their leader has).