I haven't dived the Red Sea yet so I can't strike any comparisons for you but here are some comments:
- Yes, I think you'd have a better chance of seeing Whalesharks and Mantas further up north. Near Ihambane there is a reef called Manta Reef, perhaps one of the most reliable places to see Mantas in southern African waters.
- March would be a good time of year, especially for Whalesharks and Mantas but not for Whales.
- Ponta Malongane, the spot this thread is about, is in the extreme south of Mozambique. The diving there is very similar to the northern KZN coast of South Africa.
- Mozambique has a rather limited infrastructure and flying in to places like Ponta Malongane is not really an option. You'd need to do some amount of driving at the least.
- The spots around Inhambane (Tofo, Paindane, Guinjata etc.) offer pickup services from the airport in Inhambane. This might be a good option if you're considering diving in Mozambique.
- Inhambane is still in the southern third of Mozambique. I don't know anything about diving in northern Mozambique. I know there are diving operations around Pemba and in the Quirimba archipelago but I don't have any info on that.
Hope that helps. Enjoy your visit to Capetown and hopefully Mozambique.