It does not matter which commander I select, neither the lowest nor the highest, be it navy, ground or science, it does not matter if I flag or unflag eligible or available, no academy ever appears to be selected. I cannot assign a commander to something that will not even appear in the selection window, regardless of what I do. Meanwhile, I have ten academies on my planet.
I have no idea 'who' the commander of my academy is, or even 'if' they have a commander.