You can't use Afterpay for to pay for Qantas flights anyway so this wouldn't apply.While you can double dip by paying with Afterpay + paying off Afterpay using your credit card, if you have a QFF direct earn card, I've found that most offer 1 additional point per dollar when paying for Qantas services. This means there's no real advantage to using Afterpay (except the 500pt sign up bonus).
You can use Afterpay with Jetstar, but most of the cards you refer to don't offer the extra points on Jetstar spend, only Qantas.
The 'double dipping' referred to here is normal everyday purchases where you would just be using your normal credit card, but where Afterpay is accepted. Allowing you to earn 1 point per dollar on the Afterpay transaction itself, then x amounts of points per dollar when you use your points earning CC to pay off the Afterpay balance.