A nimitz class aircraft carrier has three captain ranked officers, the CO, RO, and XO, for the operation of the ship (there are a couple more in the air group). In macross, the full SDF sized carriers seem to be about equivalent in importance (justifiable to have its own flag officer at times)Based on that, Elysion would probably
only merit one captain rank officer, with a couple commanders for the arm ships. I'm not hip to the japanese, but johnson may not even be captain rank, he would still be called captain since he is in command.
Then again, elysion only seems to support 5 aircraft...so maybe aether and hemera are just empty shells when the big guy is out