I touched on this answer in this thread, and I discussed the OAU charter and Cairo Declaration here. This thread focuses mainly on the formation and adjustment of borders in french Africa, but I do touch on origins of anti-colonial nationalism in the WW2 era.

Those answers amount to this observation: the leadership of newly independent African states were interested in either promoting a coherent Nigerian or Tanzanian &c. national identity, or were interested in a pan-african unionist project. By and large, political leaders feared and opposed "tribalism" and sought to equate it with backwardness, while multi-ethnic nation-state and cross-ethnic national solidarity were vehicles to modernity.

At the same time, Marxist or Maoist revolutionaries also condemned tribalism or ethnic chauvinism. For example, here is a Muleleist manifesto from les Cahiers de Gamboma, from 1965:

Tribalists think, more or less consciously, that the men and women of their tribe and clan are superior to others, and that as a result the others should serve and obey them. The tribalist tries to impose the hegemony, the predominance ol his tribe and his clan. In practice, tribalist ideas and feelings are used most often to create a clientele who can help them to satisfy their selfish interests and ambitions. Tribalism is expressed in different forms, of which the following the main ones:

1 The tribalist constantly exaggerates and boasts about the qualities, merits and good deeds ofthe people ofits tribe and its clan; on the other hand he refuses to recognise their faults,and even tries systematically to hide them. With respect to other tribes, exactly the opposite attitude prevails [...].

2 The tribalist indulges freely in liberalism and favouritism towards the people of his tribe and his clan [...]. By contrast, he is in general very sectarian towards people of other tribes and other clans [...].

3 The tribalist tries to grant all the privileges and posts of responsibility to the people of his tribe and his clan [...].

4 Conversely, the tribalist seeks to exempt his own people from their duties and obligations, from any difficult work, or from the most dangerous, difficult or humiliating missions

5 The tribalist practises this favouritism in the division of material benefits and the distribution of services [...].

6 Occasionally, the tribalist even believes that those who are not of his tribe and his clan are too rich and fortunate to deserve his help [...]

7 Some extend tribalism as far as preferring marriage between black women and white men to marriage between tribes [...].

8 In politics, the supreme expression of tribalism consists of demanding the formation of so-called independent republics which in fact have a tribal basis; failing this, tribalists demand ‘federation with regional autonomy’ with the distribution of political and administrative power following tribalist lines.

So, you have both Nationalist leadership and Marxist/Maoist revolutionaries condemning tribalism as obstacle in the path towards liberal nationalist or socialist modernity (respectively).

Nationalist leaders adopted a variety of strategies to contain or channel ethnic consciousness. For example, colonial Northern Rhodesia the territory of the Lozi monarch (Barotseland) was treated as a protectorate, associated with Northern Rhodesia but granted substantial autonomy. When Northern Rhodesia gained independence in 1964, President Kenneth Kaunda quickly negotiated the Barotseland treaty of 1964 which amounted to continuing recognition of autonomy of Barotseland.

On the other hand, in Algeria, the 1962 constitution declared the national language to be Islam. This led to a systematic program of enforcing Arab language education in schools, and use of Arab language in public life. This program led to the "Arabization" of the substantial Berber minority, and a backlash in the 1980s with the rise of Berber rights movement.

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So, all of this is to say that despite efforts of Liberal Nationalist, Maoist or Marxist Leninist governments to get beyond tribalism, and encourage people to think in terms of national or class consciousness; ethnicity continued to have a political logic. With the ratification of the OAU charter and Cairo declaration, national governments pledged themselves to the principle of only adjusting national borders through mutual agreement from the respective states involved. No military conquest to adjust borders.

In that scenario, the process of negotiating border adjustments to either bring the territory of an ethnic group into the state, or to cede territory (thus excluding an ethnic group from your state); would have been seen by the public through the lens of ethnic political calculus.

To use a hypothetical example: the state of Cameroon entered independence with a heavily Muslim population in the north, and a Christian or Animist population in the south of the country. At independence, leaders from the Northern, muslim portion of the country had power in the country.

Now, let's imagine that the Fang population in the south of Cameroon would like to live in a state with kinsmen in Equatorial Guinea and Gabon. Gabon and Equatorial Guinea are on board to adjust the borders.

However, the non-Fang population in the south, and their politicians, all oppose the deal in Cameroon. They decry it as a trick by Northern politicians to weaken the southern opposition, and castigate their Fang colleagues for leaving them out in the cold.

The deal goes through, but now with a politically weaker Southern population, the Baka and Gur also want to exercise the "exit option" and become part of the Central African Republic. But let's imagine that the government of Central African Republic is uninterested in negotiating, because Baka and Gur are opponents of the current government and that would strengthen Baka and Gur power.

What are the Baka and Gur to do now? Do they secede? OAU and Cairo declaration pledge African states to oppose secessionism. And there is some doubt about how viable such a small secessionist state could be.

Or, from a completely different perspective. What are we to make of populations like the Fula/Fulani? They are primarily herders, and their populations and herds move, and cross borders. Ditto, the Tuareg exist across borders in Mauritania, Mali, Algeria and Niger.

There is also the issue of what to do about ethnic diasporas who live in cities. Immediately before the start of the Nigerian Civil War, there were pogroms against Igbo bureacrats and merchants who lived in the Middle Belt and in northern Nigeria. In an imagined scenario where Biafra seceded peacefully, what would be done about this Igbo commercial diaspora living outside Biafra? Would they be repatriated? We can look to the historical example in Uganda and Tanzania where South Asian merchant communities were persecuted or forced into exile for being "outsiders" who threatened African merchant enterprise.

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So, that is the logic of the Cairo declaration of accepting existing borders, and many African leaders probably supposed that seeking border adjustments might inflame tribalist sentiments.

However, there is the example of Somalia, which is the big exception. Somalia sought to encourage secessionist movement of ethnic Somalis in northeast Kenya from 1964-1967 in the Shifta war. Later, in 1977 Somalia invaded Ethiopia in order to annex the Ogaden region which had an ethnic Somali population. Both of these actions were in pursuit of the idea of Greater Somalia. However, these actions managed to anger Kenya and Ethiopia over Somali expansionism and drove those two countries into alliance with each other to thwart Somali aims.

Both Kenya and Ethiopia wished to keep Northwest Territory and Ogaden region as part of their states, despite viewing the Somali population of these regions as subversive elements. Partly this was a concern with natural resources in the region, partly it was a belief that the population could be Kenyan or Ethiopian as long as they kept in line. Partly it was a matter of national honor, where Haile Selassie or Jomo Kenyatta would not want their respective countries to be smaller. In the case of the Derg in Ethiopia in 1978, their Marxist-Leninist reaction to socialist Somalia invading was 1) feeling of betrayal that a socialist neighbor would put the Derg's nascent revolution in danger by invading. 2) that Siad Barre was a national chauvinist who would suborn the greater goal of spreading socialism in East Africa to the lesser goal of creating a larger Somali state. In the Derg's analysis, nationalist chauvinism was a deviation from the goal of transcending ethnicity and achieving socialism for all.