Paul's response seems to most astutely answer the main question.
Seems Permaculture is a system for design based in ethics. Seems it's open to interpretation. Seems there are plenty of people who include aquaponics in their interpretation (especially in warmer climes).
As to the fine tuning, I have seen a few systems here in Wisconsin, Growing Power included, and I've yet to see anybody running a system that balances inputs and outputs. There are some VERY impressive systems. The most impressive I've seen was at the Montessori school in BayView, Mikwaukee, WI. That said, it is an education tool, and even its designer believes it isn't scaled to an economically viable size (energetic inputs and outputs aside...they are grid tied). In short, they are all education tools (the systems I've seen). This isn't to downplay them- they are fantastic teaching tools- showing a "closed loop" system in one room, one with which students can interact is super powerful. It can change the whole paradigm of thought. They just aren't viable food production systems as far as energy input/outputs are concerned (in this climate). I'd also like to say that the system at Growing Power has some significant issues. It is SUPER cool, and is the system that turned me on to aquaponics, but it's not a poster child for a viable temperate system in my eyes.