The 21% represents an "advisory fee" for which "the company [CSR] will not require any proof of delivery of the above services". I don't think that this implies a recurrent payment - R10m is the amount per locomotive. 

I guess one cannot say for sure what this means. But the most likely case according to the article is that the amount represents the proceeds of corruption. Perhaps there is another explanation, but that explanation must be the most probable one fitting the other facts in the article and what has been revealed about the Guptas in the State of Capture, the Unburdening Panel and Betrayal of the Promise: How South Africa is being stolen. A partnership fee therefore is a poor fit (especially since it's called an advisory fee).

Of course final adjudication on the matter is going to be hard to come by given the complete lack of enthusiasm to investigate the serious allegations and even if the matter reaches the courts, there's the expert  delaying tactics that we can expect.