One of my players is playing a rogue Trader crew Ace who is attempting to steal the identity of a missing naval admiral.

It's relatively uncontroversial that when he attempts to wield his authority he is using two checks:

He rolls deceive (taking penalties if the target has common lore: Navy or scholastic lore: War) to see if they believe that he is who he claims.

Then he rolls command in order to force the poor fools to accept his leadership.

Frequently however, this leads to him ordering military personnel to disobey their actual orders and do what he tells them. In such a case, should I make it an opposed test versus the command skill of the troops commanding officer? Or should I just keep the flat command test with his check receiving penalties based on who gave them the orders?

The second sounds better to me since he's overriding the other commander's passive authority. Therefore, it's more of a test on how willing the naval crew members are to listen then anything the other commander is actually doing.

If he were there it'd definitely be opposed, though.

Frequently however, this leads to him ordering military personnel to disobey their actual orders and do what he tells them. In such a case, should I make it an opposed test versus the command skill of the troops commanding officer?

I'd say no.

Every military system have a rules to solve such subordination issues. Common practice is "every top officer can normally cancel lower rank order". With common exception about ship capitan who can give contradicting orders by his capitan authority.

So if they believe he have a right to give such an order it's not matter were they ready to excecute an order from their previous superior, and such right is something written in codes.

If subordinates didn't want to excecute their latter order I'd give bonus for Command, and vise versa.

UPD: By the way, good moment for opposing command check may be try to relieve starship capitan from command, if that capitan refuse. Then command will meet two authorities clashing - top officer code authority against capitan authority (that's the highest authority on ship).