The answer is unfortunately there is no way to get BA to issue a single PNR with the Avios 2-4-1 and cash regional flights on one ticket. It is a real pain, but it is what it is.

And yes, if you could buy a single ticket so that your luggage is transferred then you use the international (airside) transit route within JNB and your bags are transferred for you; you never enter SA. (SADC doesn't affect border control / immigration). With separate tickets and luggage, BA won't check your luggage through and so you will have to enter SA at JNB, collect your bags, walk through customs, walk round to Terminal B check in desks for BA regional, then walk back to Terminal A security for your international flight to WDH. If you could manage hand baggage only (meeting the BA JNB-WDH requirements) then you can use the airside transfer route. Even if you can't get your boarding pass, there are airline desks in the transit area. You go through a passport and document check, but you never formally enter SA.