The commander's alcohol is really just soy sauce. When he goes out to drink with his troops and they all get drunk together, he manages to have fun and stay sober by drinking down a tasty, non-alcoholic pint of soy sauce.
Soy sauce also happens to be the Shougun's (しょう) favorite drink. Unfortunately, he can't just tell people he likes drinking glasses of soy sauce, or they'll look at him weird. Instead he orders it as a commander's alcohol too.