It makes far more sense to me that there should be no question of GST on a replacement item under warranty.
You buy item A and it breaks.
You ask the manufacturer to replace item A. It does so.
You have not bought a second item A. All you have done is swap your broken item A for a new working item A.
Customs should really just make a statement that items replaced under warranty are not subject to GST. If you took item A back to (say) Noel Leeming and they replaced it on the spot with another one from stock, they would not then charge you GST.