For reasons such as stated in the OP, is why the population counts are always given as an estimate and this doesn't Resides only in Africa, it extends across all the other continents with exception of the Antarctic.
There is no way you can get the accurate population of a continent or even country at any given time. People die as much as they arr been birth. Not to mention, there are tribes that aren't accessible (either landlocked or are just left alone because they haven't been contacted).
I have basically 0 knowledge of how they do a census in Africa, or if there's any scientific method at all to learning the population of Africa. I would however believe that the population numbers are hilariously wrong.
A head-to-head count is what goes and the results are always going to come out wrong due to factors as stated in OP. These counts aren't done all at once and as to the fact, some persons are usually not available at the time, some others are counted twice and some others aren't accessible. Hence, we just rely on estimates to get a possible result.