Terminal A is the international terminal, so both LHR and BBK flights will arrive and depart from there. You only need to clear security, not immigration.

I don't know if BA will interline to Air Botswana, but with that connection time, why risk it anyway?

There is always talk of theft at JNB, but I personally have not had a problem. I'd just use sensible precautions and not pack anything you cannot afford to lose or which won't be adequately insured.

Comair carry-on allowance is same as BA allowance.

On the lounge question, if you are connecting to a BA (Comair) flight from a CW Long haul, you can use the lounge (even if on separate tickets). Air Botswana are not a One World airline, so no lounge access.