My understanding (which may be totally flawed) is that the TPM (ticketed point mileage) which is the mileage IATA uses when assessing whether a trip comes within the MPM (maximum permitted mileage) for a particular itinerary is assessed at the minimum actual flight distance for the route.

So the SYD-LHR mileage for ticketing calculations is not the GCD (great circle distance) between Sydney and London but the combination of the distances of the shortest route by sectors eg SYD-HKG-LHR or SYD-SIN-LHR or whichever it might be. If there are non-stop flights between BNE and LAX (or they have existed at some point) then the TPM will be the direct GCD. But if there have never been direct flights then the TPM will be the combination of the shortest sector combination that exists (? has existed) whether that be BNE-SYD-LAX or BNE-AKL-LAX.

The TPM is actually something that can change. When the 747-400 brought in the reality of flying non-stop SYD-JNB the TPM dropped from the sum of the sectors SYD-PER and PER-JNB to the GCD SYD-JNB.

So getting back to the original point of the TPM for the SYD-SCL flight because no airline flies (or ever has flown) that route non-stop, the TPM used in calculating itinerary distances will be the shortest combination of sectors on that route ie SYD-AKL-SCL.

Be thankful that LAN Chile didn't stick with its original South Pacific routing and charge you SYD-AKL-PPT-IPC-SCL