Saves: https://drive.google.com/file/d/1WNP2MhECrJ49dTKYAVRv73UI2FUs4oF9/view?usp=sharing
It is not possible to promote the Commander to "Admiral", "Invader", "Privateer" or "Exterminator".
I have all the necessary resources and my ideology is indeed "Malevolent".
I obtained the Commander after building the "Temple of Despair" improvement.
Promotions not available.
Malevolent Ideology.
Temple of Despair.
Edit: More details on bugs after promoting the Commander in this thread.