"It will be borne in mind that this is not a question of the power to proclaim martial law when war exists in a community and the courts and civil authorities are overthrown. Nor is it a question what rule a military commander, at the head of his army, can impose on states in rebellion to cripple their resources and quell the insurrection."
What do you think they meant when they made these exceptions?
That the military authority, at certain times, does supplant the civil one. The Constitution still governs them both though in any and all circumstances without exception.