To exercise the Australian rights to operate flights between Australia and Indonesia, you have to be a majority Australian owned airline. Indonesia has their own requirements to exercise their rights.
Tigerair was a majority foreign owned airline before it was bought by Virgin Australia. When Virgin Australia purchased the airline outright, Tiger remained a majority foreign owned airline. Virgin can push this issue, but the Indonesians may start to look more closely at the VAA / VAI corporate structure and determine that VAI is nothing but a shelf company owned and controlled 100% by a majority foreign owned entity in VAA.