Soy Sauce
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.
The next time you go to a bar, order yourself a commander's alcohol. It's like saying you want a Roy Rogers or a Shirley Temple, except it isn't pretty and it tastes horrible.
しょう
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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.
Picture the Shougun sitting on his throne, guzzling down some salty, brown soy sauce. It's splashing on his robes and the smell is making his assistants gag.