Note: While I have tried to be careful with my selection, given the age of several the responses linked below, they may not meet the current standards r/AskHistorians expects of responses. If that is the case, I apologize.

It's important to note that "sub-Saharan Africa" is a massive, incredibly diverse region. Each region/country has its own history with Christianity. Grouping together the wildely diverse Nigeria, Ethiopia, and Congo-Kinshasa/Congo-Brazzaville (to use your examples) would be a massive undertaking if we are to successfully explore the nuances of Christianity in each of those countries, not to mention the other 50 or so countries in that part of the world.

While African Christianity is often associated with 19th century European missionaries who participated in colonial efforts, the religion has a much longer history on the continent. Notably, you have Ethiopia, which had large Christian populations for more than a thousand years before modern Europeans began their conquest of Africa. Some older posts on this topic include:

u/Commustar discusses Ethiopia's early adoption of Christianity: https://www.reddit.com/r/AskHistorians/comments/23awea/why_did_ethiopia_adopt_christianity_so_much/

u/Compieuter offers and discussion of what medieval European Christians though of Ethiopian Christianity: https://www.reddit.com/r/AskHistorians/comments/77tmgv/what_did_european_christians_in_the_middle_ages/

Here we have u/AgentIndiana discussing a supposed lack of missionary tradition among Ethiopian Christians, with the questioner wondering why Ethiopians didn't convert other African groups: https://www.reddit.com/r/AskHistorians/comments/b3rdo7/why_didnt_ethiopia_spread_christianity_into_africa/

Finally, here is an older discussions of the role Christianity played (if it played a role at all) in sparing Ethiopia from colonization, with contributions by u/RioAbajo, u/CheekyGeth, and others: https://www.reddit.com/r/AskHistorians/comments/3fbhiz/was_ethiopia_not_initially_colonised_due_to_the/

It's interesting that you consider colonialism to be an "unnatural" way for a religion to spread to a new location. That feels to be more of a subjective, moral judgement about how religion "should" be spread, a belief which says more about our modern secular notions of religion and society than it does about the places and times you with to examine.

Here u/Alkibiades415 offers a reading list for the relationship between imperialism and religion: https://www.reddit.com/r/AskHistorians/comments/l3v76i/where_to_start_learning_about_religion_and/

u/Starwarsnerd222 offers some discussion as to why British West Africa became Christian and the British Empire's "crown jewel" (India/Pakistan) did not: https://www.reddit.com/r/AskHistorians/comments/m5pwss/during_british_imperialism_christianity_became/

While this question shifts the focus from Africa proper to the African diaspora, u/uncovered-history discusses why African slaves and their descendents in the United States did not reject Christianity: https://www.reddit.com/r/AskHistorians/comments/8o4jbi/why_didnt_freed_slaves_reject_christianity/. While we can't simply copy-paste from the American context to the African context, it does provide some insights as to why the religion of "oppressors" (such as slave owners or imperialistic conquerers) might hold appeal for those being oppressed.

Hopefully that collections provides you some insights to begin answering your question.