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It's because the commander in chief has a responsibility to safeguard the authority of the office of the President IAW the separation of powers. As you have remarked, there needs to be an orderly transition. If some judge can bark orders at the military and force it to rearrange its priorities (to effect immediate implementation) on this issue, judges could do so on other issues for whatever reasons. It would set a precedent that undermines the power of the Executive branch.
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