Things have definitely not changed. It is never possible to through-check bags to another South African destination when arriving via Johannesburg, and it is a legal requirement to collect all baggage, proceed through customs, and then re-check separately for any domestic segment. This is unrelated to the ticket and applies to all passengers, on all tickets whether separate or single PNR.

When travelling outbound from another South African airport via Johannesburg, it has always for me been possible to check-through (including on flights in the last few months). I do this when checking in for SA domestic British Airways (Operated by Comair) flights, always on separate tickets. I do not know if it is Comair’s policy to always through-check to London, or if I have just been lucky on every occasion.

Comair tend to be more forgiving than BA mainline in general. For example, I have missed connections multiple times on separate tickets inbound to South Africa, due to either a late inbound or a long immigration queue, and British Airways (operated by Comair) have happily placed me on a subsequent flight at no charge. I have never risked a similar outbound misconnect from South Africa! As I feel it may very well result in a much less fortunate outcome.

So, all in all, I suggest for anyone reading and considering separate ticketing — feel comfortable booking separate tickets, but with the usual common-sense cautions and appreciation of risk about misconnecting. Be aware you must always collect and re-check bags when travelling into SA, regardless of ticket. Be aware that anecdotally, Comair tend to be helpful if a connection is missed inbound, even on separate tickets; and that they tend to happily check bags through when leaving South Africa. For this reason - and because domestic tickets are usually available for a reasonable same-day price, I am always much more conservative about connection times when leaving South Africa, than when arriving.