So, just wanting some clarification here.

Is "union commander" a typo, and perhaps you meant confederate commander?

Or is "commander of the army" a misunderstanding of Lee's role as a senior (though not general) officer of the U.S. Army in the time before the Civil War, for example when he was fighting in the Mexican-American war?

To the best of my knowledge, Lee was only a Lt. Colonel before his appointment to command the Confederate Army of Northern Virginia. And though he obviously commanded "forces", I don't believe he technically commanded "an army".