I believe the airline validates your visa status (using the Advance Passenger Processing system) which is done prior to check-in (maybe rechecked then too, I dont know). Your visa/ETA is electronically attached to your passport used to apply for it.and then to your ailrine PNR when you enter Australia. So the system does know you left within your visa/ETA conditions and you should have no problem. I'd guess you aren't the only pax to do this, but they do like you to use the same passport on exit.