Well, it looks like I missed the news that EK has very recently begun a new Skywards miles devaluation, which has yet to apply to return bookings, and that the miles calculator has yet to be updated — it explains this discrepancy perfectly.

As a workaround, I am considering making a return JNB-LHR booking, taking the upgrade at a lower mileage rate whilst it's still available, and then calling up EK to change the return leg to depart from MUC instead of LHR. EK phone support indicates that this should work fine.