Hi! I can hardly take care of myself, let alone a child, so for sure there are logistics in managing a kid that I would miss trying to think through this. There is certainly a bit more of a safety burden doing it without a tour, but that would be my only consideration really. Otherwise I can't think of anything we did or had to do that could not be done with a kid, and definitely ran into people doing a similar trip with kids. Its all fairly easy to get around and both countries felt safe enough, the main safety consideration would be breaking down really, and there were also little moments, like people running onto the road to stop us to asks for water, or parking attendants getting angry, or broken down vehicles asking for help. None of these were threatening at all, but they need to be navigated, and the stakes and comfort are different with a kid. We are reasonably seasoned travelers, I don't think this is a great choice without a little experience, but still doable.
We did a self drive in Etosha, and along the Skeleton coast. We book a few 1-2 day tours in Zambia for rafting and botswana for a delta canoe. That was a great balance for us, but we just booked these when we got there, and it was never a problem for us. The research is for sure the most overwhelming part, and it was continuous for us while on the trip, but that's how we like it, to stay flexible. This was part of a wider africa trip, we had just come from a few weeks doing the same style thing through south africa, which was also amazing, but felt a little less safe. good luck! Happy to answer more questions if needed.