For all its claims of not being a military force, Starfleet certainly depends on rank and respect among its officers and crewmen, so this sort of exchange comes as second nature to Deanna. She waits patiently at attention while he finishes his reading. Whatever he is reading may be important - or he simply wants to remind her of her position. Either way, she isn't particularly offended by being made to wait.

When he offers her a seat, she nods again before taking it. "Thank you, sir."