A couple of points which will hopefully clarify and guide:
1. The SC calculations in MM are typically distance based (I.e. Between X and Y miles distance will earn Z SCs)
2. I am not familiar personally with QF SC earn rates or any changes to these. Feel free to point me at a concise summary of any changes and I can do my best to ensure MM reflects these
3. Implied in your post is that QF have different earn rates for their own metal(codeshares) than on others. Or perhaps different booking classes within the same cabin can result in different earn rates. As there is no way for you to tell MM what carrier you have chosen for a sector (often multiple carriers will serve the same sector) it is not possible for MM to take this into account. Nor does MM know whether you are booking into J, C, D, I etc.
I'm happy to update/correct MM if I can be pointed at a definitive reference for the change (plus a concise summary/interpretation if needed), and providing of course it is possible to do in MM without extensive rewrites (which I don't have time to do). Please feel free to share any relevant links in this thread!