Would Philip II personally commanding the Armada have helped?

Would the Armada's outcome have changed if Philip II had commanded it personally after Santa Cruz died?

Probably not: the king's authority might have improved obedience, but the underlying invasion plan was strategically unsound.

Philip II would have outranked every competing commander, removing disputes over which noble or professional officer should lead. He might still have retained Medina Sidonia as an organizing chief of staff while using royal authority to compel obedience. That arrangement could have improved cohesion aboard the fleet. Even so, royal presence probably would not have cured the invasion's strategically unsound design, especially its dependence on coordinating the Armada with Parma's trapped transport force.