I think we may have mistaken the MGSV Phantom Pain map size.
Initially we used this image from kojima radio to find the current map size
which appears to end up with ~4km by 4km map size.
However, on the official website, they've given us a much clearer picture, and the map size may be wrong.
http://www.konami.jp/mgs5/tpp/jp/progress/index.php5
If you look closely, the map clearly shows a size of 4km width, and at least 3 km, with ticks going into 4km.
so the 4km by 4km seems to be perfectly fine.
However, if we look closely and putting together information, we know that there's in fact two areas: Afghanistan and Africa.
Nowhere do we see on this clear map a "different area" that points to the existence of an African map.
However, if we look closely, there is a map of similar size of 4km by 4km that's placed "above" the Afghanistan map, so in fact MGSV Phantom Pain may actually have two 4km by 4km areas, Totaling 32km^2, EXCLUCING Mother Base.
This puts the total map area roughly on par with Skyrim, which has around 36km^2 not excluding impassable areas.