Does it confuse audiences that in The Caine Mutiny Humphrey Bogart is called "Captain Queeg" and "Lieutenant Commander Queeg"? Or in the various Bounty movies "Captain Bligh" is also called "Lieutenant Bligh"? Or Captain/Commander Richardson in Run Silent Run Deep, Captain/Lieutenant Commander Morton in Mr. Roberts, or Captain/Lieutenant Collins in The Sand Pebbles? I don't think the audience would think twice about it actually, if a writer cared to write it that way. It just seems they default to captain rank for the captain position.
But none of those had executive producers who assume the worst of their audiences.