I don't think this would be as impossible as most people seem to think. The Romans used to base the administrative districts of their provinces on pre-existing tribal boundaries; just having their colonialist descendants copy the idea, and voila.
That is true, but the Romans actually intended to turn the areas into culturally Romanised parts of their empire. They did outright conquest, or they did vassalage. Either way, it made sense to keep existing boundaries (either because the vassal was just kept intact, or because needlessly reconfiguring the tribal boundaries op people you've just conquered is just going to cause resentment).
Europeans had little reason to care (at least to such extent) when carving up Africa. They mostly didn't aim for vassal states, but for subjected territories, and they certainly didn't intend to integrate the inhabitants as equals within their existing states. I believe that can be changed, but it requires a change in general attitude in regards to colonialism (and in particular to African colonialism). I have some trouble thinking of a convincing POD.
There are very few arbitrary lines in Africa. African borders mostly follow waterways, resources and geographical accidents, just like everywhere else in the world (except North America). IMHO to simply follow geography and economy is clearly the best way to create a viable country.
As often as not, they follow waterways that were channels for trade, rather than historic bounderies. Geographical borders make sense, yes... when applied correctly. Mountain ranges tend to be pretty useful, and often form natural boundaries. With rivers (and those were often used by Europeans), you have to be careful. If the river has historically been a boundary, that's great. But if a river is a centre of a cultural area, with the same people living on both banks, turning it into a border is terrible. And that happened regularly, too.
Best boundaries are ultimately cultural boundaries. Let people decide who they are, with whom they wish to share a geographical territory, and let them have that territory. In the end, this often resembles something geographically sensible (as with mountain ranges dividing different peoples regularly), but the goal should be to ensure that peoples who feel they ought to be joined must not be divided, and people who feel they ought to be separate should not be forced into one country.
Bottom line: borders shouldn't be drawn by outside forces. Even if they follow geographical features, these may well be the
wrong geographical features, which still makes them random lines. Just... more squiggly random lines.