I'm not very knowledgeable on the subject of encoders, but I believe there is a program called faac for aac encoding. But if you're encoding a whole mp4 movie, you may want to use mencoder (associated with mencoder). I've not tried mp4 but I'm led to believe they are supported, and I've definitely created AVIs with aac audio using it. So I would say to have a look at faac or mencoder and see if they fit your need.
P.S. Mencoder is definitely scriptable, I think faac probably will be.
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