They are separate in the sense that they are raised, trained, funded, etc. by the state government. The fact that operational control is ceded to the federal g

They are separate in the sense that they are raised, trained, funded, etc. by the state government. The fact that operational control is ceded to the federal government in times of war doesn't change that. The US military can't call up a unit that doesn't exist, or that no longer responds to its orders due to a constitutional crisis. The Second Amendment implication is that the federal government may not prevent the formation of a separate state militia. What happens after that is irrelevant to this discussion.