The article doesn't link to any of the statutes in question, so this is just a guess, but I don't think this would backfire on the FBI at all. The argument the FBI is making is that the New Zealand statute defines the activity in question as only being illegal if physical material was taken. That is simply a matter of statutory interpretation, and the fact that a New Zealand statute might only prescribe against physical material being taken doesn't invalidate US legislation that defines piracy without incorporating any sort of physical requirement.
In other words, NZ Statute A might only define something as theft if material is physically removed from the owner, but that wouldn't invalidate the operation of US Statute B which defines something as theft even when material is only transferred electronically. The FBI wouldn't be precluded from prosecuting someone on US Statute B just because they relied on NZ Statute A to obtain the evidence.
Statutory definitions generally apply only to the statute in which the word is defined, so the fact that two statutes define the same word differently does not indicate that a Court must choose only one of the two. It just means that when applying Statute A, the Court uses the definition in Statute A, and when applying Statute B, the Court uses the definition in Statute B. In this case, there is not enough information provided even to say whether it is the same word in question or not. Alternatively, laws vary by nation, so something can be legal in NZ that isn't legal in the US.