checking my paperwork from last week (Avis at JNB, booked through BA) - there were zero extra compulsory charges, I declined the Super CDW and windscreen cover so they put a hold on the card for the excess, which was ZAR 3947.37 (about 215 GBP), for a Polo.

Some people mention horror stories about SA hire car places, hitting them with made up damage, etc, but I haven't had a problem in maybe a dozen rentals in the last year. As FiS mentions you will likely get dinged for a few toll charges around Jozi, but they pass those on without markup and, like the fuel charges, they seem very reasonable to me.