It is all part of the original (and ongoing, renewable) permission given by the AFC to the team from another federation to play in an AFC league.
The exemption is based on the fact that Phoenix are classified as an Australian club located in New Zealand, but clearly not 100%....
With the demise of Bin Hamman (who used to bag us constantly) this may be resolved one day to our advantage, if FFA continues to bat for us, since FIFA hasno problem with us. This quote is (via Wikipedia) from a Sepp Blatter interview with Les Murray on SBS TV in 2008:
"It is not the matter of the Confederation, it is the matter of the FIFA Executive Committee... If Wellington will go on play on in Australian League, then as long as Australian league wants to have them and Wellington wants to stay (and) Both association in this case, New Zealand Soccer and Australian Football are happy with that, then we will give them the blessing. The Confederation can not interfere with that."