They would have a compelling case.
Both carriers will now need to address additional criteria under Section 9 of the IASC Policy Statement. The 'competition criteria' is a key part of that.
Virgin currently have 4924 seats per week to Indonesia, just under 20% of the allocated capacity. The Qantas Group have 20,076 seats. On those grounds alone, I find it hard to see how the commission could justify giving a lion share of the capacity to the Qantas Group, as it would further entrench their dominant position in the market. Even if they were to evenly split the additional 5000 seats, it would only increase VA's share of the capacity to 24%.
On the other hand, I can also see them prioritising the routes currently unserved by the applicants. I.e., PER-CGK for QF, WSI-DPS for JQ and PER-DPS for VA. There is a case to be made for Jakarta, given it would diversify Aus-Indo options beyond Bali.