Why not Sydney? Is there more hotel quarantine capacity in the other cities?
That was the case with the Nepal private charter of AU travellers that returned recently. The Commonwealth would not issue a permit for a SYD arrival to spread to quarantine load and but a permit was issued for BNE.
It really comes down to logistics and where there are QF crew and quarantine accommodation and related security.
Note that each State is responsible for the quarantine costs of its own residents irrespective of the arriving port and host state.