I would imagine it has nothing whatsoever to do with commercial alliances and everything to do with weather and air traffic conditions.
I fly KLM from Schiphol to CPT fairly often and the route varies similarly. In the same way, departures out of CPT to Europe often turn south and head across the peninsula going overhead Constantia and then up the west side of the peninsula, but for the last couple of days they've been heading north and tracking over Bellville and out to sea near Blouberg.