The time with the rookies makes hearing 'sir' normal. The fact that he's currently got the best equipment, the best plan, the best AI (delta has a warm little pulse of pride at that), makes SENSE that he's sir. That he's in charge. They need guidance.

Look how lost they'd gotten without him?

"Load up. When Carolina gets here, have her do the same. Find transport with the most storage space and fill up. Wait for me." He'll be busy rigging a bomb somewhere. "Then we move out."