The miles that are credited to accounts are all GPS based using fairly accurate data and likely not assuming that Earth is perfectly spherical.
I say that because it is the methodology written up by gcmap where I've found matching MQM accuracy down to the mile.

The discrepancy of Delta's itinerary comes from using a different database of distances for airport pairs. Probably two different people coded up the itinerary and the skymiles accounting and they couldn't be bothered to match.