Africa is ill-represented in the first place
If it makes you feel better, it has never been represented well in any Paradox game. Even in EU1, North Africa was just a poor region where Spanish would continue their Reconquista for the lulz (if they even bothered). There are complicated reasons for this, but it all boils down to either the area is too easy to pacify (unrest in Algeria in the 19th Century? What's that?), is so poor in money and manpower that it cannot defend itself, or some combination of both. EU4 has tried to make Africa as a whole more vibrant, but the great irony of the entire Paradox line of strategy games is that their Euro-centrism makes it hard to depict the complicated nuances of places like Africa and the Middle East. (And there are times when it goes the other way, and you see North Africans doing crazy stuff, like conquering Italy and Islamicizing it within a decade or so....)
In CK2, it's not quite so bad (there are some nice counties if the AI can be bothered to utilize them well), but I kind of agree with your post about the Qabila that there is a lack of depth in the Islamic world, which causes them to either be too powerful or too weak (depending on current expansion).
I do have a question for you, though. Let's postulate a medieval world (say, around 1270) where "crusaders" under Saint Louis actually seize Tunisia and conquer the entire region (per holy war CB in CK2) and not the just city itself. There are obviously tribes living beyond the frontier of the de jure duchy (CK2's unmodded map), as well as an entire political apparatus left over from the previous rulers. How would a bunch of feudal Western Europeans even begin the process of pacifying or crushing the tribes that border the region? Is it even feasible? And if not, then are we back to the problem of permanent terra incognita being used to prevent bizarre conquests and ahistorical economic development?
EU: Rome had mechanics for barbarians in unowned provinces. They were unplayable factions that would build up barbarian power (read as population) and then spawn barbarian hordes that would attack settled (read as owned) areas. Punitive expeditions could be undertaken to wipe them out before they launched their own attacks (a steady source of slaves). Actually colonizing the provinces was difficult and time consuming (you might not colonize the map before the game was over), and it had some drawbacks (some players preferred farming barbarians for slaves and freeman to colonizing the interior of Europe as adding provinces hurt research speed without corresponding increases in citizens).
This worked in depicting Germania and the periodic migrations/invasions of the Roman world. It also worked, because it more or less took these provinces and population out of circulation. They existed on the map, but you really couldn't conquer them with any real speed. This is one of the issues at play: even if you added the entire Sahara with tribes and nomads and whatnot, you open the Sahara to conquest, as any county on the map is available for ownership by anyone else (even with penalties if your government doesn't mesh with the holdings in question)
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