The only advantage Mt Isa has over Townsville as a break of gauge point is saving around $3-billion to extend the standard gauge further east. And while standard gauging the entire corridor to Townsville makes sense, if the new Tennant Creek to Mt Isa line costs - say $2-billion - the NT and QLD governments are likely to decide that's all they want to spend - and adding more costs on is likely to kill the project.
Most of the cross-border freight is road freight from Brisbane to Darwin via the Warrego Highway A2 corridor. Rail freight from Brisbane to Mt Isa has to go the long way via Townsville, but there is some doing that. Containerisation makes Mt Isa an equally effective break of gauge point as Townsville without additional rail construction, and at the moment the only real tonnage potential for the Mt Isa/Tennant Creek line is several proposed phosphate mines and the concentrates originating in South Australia and the NT heading to Mt Isa for processing. Mt Isa remains 600km closer to Townsville than Darwin, so it's hard to see how much existing mineral traffic from the North West could actually be captured competively by the Darwin Port...particularly when each of those mineral producers has built their own train and ship handling facilities at the Townsville Port.