Okay, Soixie, I don't see it as a bug.
First of all, a commander-in-chief can appoint any of his alliance commander-in-chief, why do you think it should be prohibited if the account is a substitution? Why do you think the one who assigns the role should know that it is a substitution if the user himself does not want anyone to know?
Second, the action control limitations for a substitution are a game safety policy to prevent a person from accidentally taking actions that would harm the alliance or the original player himself.
And yes, the solution is as you well indicate, you have to enter with the original username / password, deactivate the substitution and make the options that the player wants. (And optionally give subs again)
