You have a valid question.
Does he have to go through Kelly or Mcmaster in the new dynamic? Don’t know. Shouldn’t have to.
While very important, I do not think this collision needs the Sec Def to talk directly with the President. Most likely the SecDef or someone from his office would call the WH and inform the Nat’l Security Team about the collision and they in turn would tell the President. Not all serious or important events require a direct communication between the department head and the President.