Thank you for your service to our country and the State of Mississippi in particular!
Your description is accurate in every point as I understand modern military protocol. The example you gave came to mind as I was preparing my post, but it didn't seem to fit because the Confederate government had only limited authority to 'Federalize' any state unit. The law concerned service obligations of free white male citizens. If a man was eligible for military service under the law, his enlistment in a state unit was of no consequence to Confederate authorities.
Individuals subject to regular service could be literally taken out of the ranks of state commands. Officers frequently combed rolls of state commands in search of men who should have been in the Confederate army. If a man believed he had been unjustly forced into service, he could seek redress through the court system or desert. In either case, until the courts acted the man in question would answer to Confederate military authorities and be subject to their orders.