Fr Flannery can’t have it every way
His public displays of disobedience are petulant and foolish, it only gives ammunition to newspaper media to exploit and create even more wedges and hammers to knock the Catholic Church with. He knows there are other ways.
Be intellectual if he wishes, but it is obvious that there are events of Catholic teaching which are no go areas, accept it, live with it, obey it as was one of his initial vows. If his conscience doesn’t allow him to do so, then he might find it easier to leave the comfort of his Redemptorist Order.