Hmm, I never do my reconcillation through the ATO, but the FAO sends it to the ATO to pay it and it gets paid with any return. Will that be different now and it will be paid by the FAO separately? Hmmm.

I haven't been this confused since the FAO told me they owed me $18,000! LMAO. Thankfully they never paid that amount because I knew it wasn't true, but no one at the FAO could tell me why it was saying that.
FAO will still send the payment to the ATO as it's Commonwealth payment and if you owe money to ATO, it will be paid from FAO moneys, and vice verse. the difference will be that your FAO money will ONLY be calculated by FAO, no more guesstimates on your tax return by ATO (if your accountant ticks a box that says you haven't claimed any FTB through the year, when you have, it will tell you your full annual entitlement - not just the top up you're due - hence the dramas with paying too much!)