nhorley - If you are thinking of flying in Europe, you have answered your own question when you said "Beyond the obvious point of making sure that one's quals match one's intended employment". A non JAA CPL gained in SA will be as useful in Europe as a non-JAA CPL gained anywhere else.
The SRG website is down at the moment so I can't check but I believe that there is only one school in SA that is anywhere near being approved for JAA CPL training. Called something like the Flying College of South Africa, it's run by an ex-CAA Flight Examiner and Flight Ops Inspector. I have no idea what courses they offer, you will need to check on the SRG website when it's back on line.
43rd Air School is not approved for JAA training and BA most certainly do not send their pilots there. BA trains only at Oxford, Western Michigan, Jerez and ATP Academy. Beware of inaccurate sales pitches masquerading as helpful information.
If your intended career is in SA, you have your choice of schools.