It's up to the user to enter the "trips" themselves (e.g. SYD-LHR vs SYD-SIN-LHR), and this is a limitation of the spreadsheet, but one I haven't been able to easily resolve as yet and which affects what I think is a small proportion of trips on partner airlines.
I thought this would be a pretty simple exercise but it ended up being more complicated than expected. There is a SC equivalent of this spreadsheet which has been covered on AFF before and can't be shared publicly due to "simpler and fairer". Hopefully the routes I've shared help those who want to calculate their SCs.