I like the idea, but I really like the fact that they are perks. You do not become better as a commander by being given a title. Personally I think it makes far more sense to keep the perks as perks, and making the titles relatively hollow and only affect things like set up. I also think it would be great if you can choose who to give positions, where having someone unfit to take the role gives them a negative, or having too many can be negative. I think this would be far more in touch with the realistic approach the devs are going for. The best leader is not always the best fighter.
Some suggestions along my line of thinking:
People under a commander will gain more morale bonus for watching their leader kill someone, receive a big morale penalty if their leader is wounded or killed. This can be scaled so the company leader gives a bigger bonus and penalty than squad leaders.
Prep talk: Leaders give talks before battle that can cause morale penalties and bonuses depending on their stats, experience, etc. This could also be built into normal traits, such as a leader being charismatic or bad at public speaking.
An initiative bonus for being close to the squad leader, dependent on a stat of the squad leader (prob initiative), to represent a good squad leader relaying plans effectively and therefore the squad carrying out the plans more effectively. However, to stop people making everyone in the company with a good roll on this stat the leader, giving a reduction to the squad leaders combat stats, to represent them having to spend more time paying attention to positioning etc of their squad.