It seems they updated this document again:

Department of Home Affairs - Home Affairs Minister Dr Aaron Motsoaledi provides an update on the partial re-opening of borders and services during Alert Level 1

Immigration officers will be required to assess the movement and place of origin of the traveller and not the country of origin of the airline concerned.

My interpretation of this is that e.g. German citizens can board flights to SA via AMS or LHR if only on transit at these airports.