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I have not seen a FAQ which allows any exception. If there is no such allowance, think of it as class defining aspect. If you want to Rage, then you're not going to be giving your animal commands. If you want to give your animal commands, then you're not going to be Raging. Alternatively you can give you animal an attack command before the Rage and then exit the Rage and tell the animal to back down.
If we're talking about the Mad Dog archetype, none of the gained abilities require Rage and the Barbarian loses about half their Rage powers. This reinforces the notion that Raging isn't suppose to be as beneficial to the Mad Dog.