I just played with the calculator, just the BNE-SCL part (too tired to do thru to GRU)
There are three sensible ways to get to SCL from BNE, (1) fly BNE-SYD on QF metal, then SYD-SCL direct on QF metal (2) fly BNE-SYD on QF metal, then SYD-AKL-SCL on LAN metal, and (3) fly BNE-AKL on QF metal and then AKL-SCL on LAN metal.
Due to expansion of codeshares, all these flights can be sold as either LAN or QF tickets (they recently added certain Australian QF metal domestic flights like SYD-BNE as LAN codeshares)
In my experience you will never come near to LAN pricing with Qantas. But what some sites might allow (which is what I do) is to get flights that ticket the main flight as LAN with the domestic Aussie leg ticketed as QF, or the AKL-BNE segments as QF.
Assuming Discount Y for all travel: (and using the calculator provided by eminere, except for LAN ticket BNE-AKL, which I got from the dreaded "Tables")
1.- Flying BNE-SYD-SCL on QF ticket = 10+40 = 50 SC
2.- BNE-AKL-SCL on QF tickets = 20 + 35 = 55 SC
3.- BNE-AKL-SCL on LAN tickets = 10 + 35 = 45 SC
4.- BNE-SYD-SCL on LAN ticket = 10 + 20 = 30 SC
5.- BNE-AKL on QF ticket and AKL-SCL on LAN ticket = 20 + 35 = 55 SC (this is all within one ticket purchase, they are not separate actual tickets)
So what does all this mean? Do what I do and use an online ticket service like expedia/vayama/cheaptickets/etc and you should easily get a choice where the BNE-AKL sector is ticketed as "QF" and the AKL-SCL is ticketed on LAN. You get more SC that way than buying a QF ticket on QF metal all the way via SYD!!!!! Perhaps not what the Table guru's intended, but it works for me.