I can't disagree with your conclusions.
As for the first point about militia under General Wofford's control, there's one way this could happen. That's if Governor Brown formally turned over control of specific militia commands to the Confederate government. There probably should be something in the Official Records or the Governor's papers about this.
Without the governor's release, Confederate quartermasters and commissaries would not be able to release pay, equipment, uniforms or rations to militiamen. Also, term of service could not be changed without consent of the officers and men, so they were probably limited to ninety days. within state borders, of course.
This is why we rarely ever see militia commands in a Confederate order of battle.