Upvote:3
Most domestic flights within Australia do not require you to go through passport control and do not require any identification. Taking these flights is no different from driving.
However, a small number of internal flights are actually one leg of a longer international flight. These flights are outside customs and immigration control and you need to pass through immigration twice. These should be clearly identified when you buy the ticket, but be sure to check. The clue will be they arrive and depart at international terminals.
For your visa question, it is hard to answer but remember that there is no guarantee of receiving a visa even if it appears you would qualify for one. I would suggest that you stay in Australia until you are finished with your friend rather than leave and hope you can come back.