Every time you leave Thailand your Visa is done. So no need for Visa if you are not planning on staying longer than 60 days (30 days visa excempt plus 30 days extension) in BKK. This is for the US passport.
So you applied in Australia, but you want to enter Thailand from Indonesia? Usually you need a flight from the country you are applying (Australia) to Thailand.
Last year, people had to stay up to three nights at the Malaysian border to enter Thailand again. They were travelling individual, everybody on a paid border bounce could turn back immediately.