It really boils down to this:
Without knowing the methodologies MWeb and Telkom employ to come up with these figures, you can't actually compare them. If M-Web is testing their network from within their network vs. Telkom testing it from outside their network, then obviously these numbers will display a vast difference (since M-web for example would not be taking into account IPC or SAIX -> MWeb routing).
For these numbers to be comparable, the tests need to be identical. ICASA should have indicated a standardized testing suite that all ISPs that publish KPIs have to conform to (and these tests may be annually revised) to allow their numbers to be considered "officially sanctioned". I don't understand why this wasn't done. Well actually I do, gross incompetence, but still.