The building in question was first built just after the abortive conversion of João I (in 1491). It was then further reconstructed, and greatly extended under Afonso I in the 1530s, as he prepared a campaign to spread Roman Catholicism to the countryside under a theological framework that would hew more clearly to Kongolese ideas (see Heywood and Thornton, Central Africans, Atlantic Creoles, and the Foundation of the Americas on some of this--as well as many of the other details; pp. 60-67). It's also important to note that the Portuguese living in M'banzakongo full-time never numbered more than about 70 prior to the mid-1500s, but they had outsized political influence. Their arms had helped to put Afonso on the throne, in effect, over his brother in 1506, but he sought to get out from under some of that influence. His grandson Diogo I would eventually expel them in 1555, which would not make them happy, and would not exactly last. But at the time this structure went up, and when it was expanded, Catholicism was intended to serve as a Kongolese orientating force that would elevate the Kongolese elites (and the manikongo / king in particular), so as to change the rules of the game of statecraft in one way or another. That goal, taken together with the view of these buildings as places of spiritual power (akin to charms), meant that ritual, form, and consecration all had to convey authenticity and authority. Among the Kongolese elites in the capital, the form of a church or cathedral was set in Rome (not necessarily Lisbon!), so the similarity was deliberate whether inherited from the original church or not. Afonso I in fact had restricted the use of masonry and carpentry on the European model to churches and a few nobles' homes, as the methods were not generally affordable or effective to meet the needs of most people. Thus, not every technical measure the Portuguese brought to Kongo was found to be applicable or useful in the Central African situation.

As a result, we have to consider the construction to involve a syncretic model; it was not imposed by outsiders, but built and expanded by Kongolese initiative (although we don't know whose exact design was used) for Kongolese purposes. At the same time, any design was constrained in important ways by the political and social need to show connections to Lisbon and Rome. Certainly by the 1530s a significant number of Kongolese nobles and other high-status people were literate in Portuguese (and a few reputedly in Latin) so even if the initial church were the design entirely of the Portuguese on the occasion of João's May 1491 baptism, the major expansion and reconstruction under Afonso need not have been. The fact that the style did not extend beyond churches and a few large estates indicates that the use of the design, its shapes, and its materials had a specific purpose connected to the buildings in question--to show connection to a certain religious tradition that bore royal power, and to indicate one's own personal connection to the same ascendant signs among nobles. The whole history of Christianity and struggles over theology in Kongo is fascinating, because it raised what would be recurring questions about who had the right to interpret the word of God (and claim revelation) among Christians in Africa south of the Sahara.

[edit: I should add, as well, that the church was meant to be built in a way pleasing to the sensibilities of the new co-religionists, so that is another point. There are other structures that are definitely Portuguese near the site, so it is really hard to disambiguate the influences. Even the UNESCO write-up for the World Heritage Site here--pdf warning, y'all-- stops short of attributing it.]

[edit 2: I've been looking for any detailed physical description, contemporary or archaeological, of the out-buildings this structure assuredly would have had--as a recognized cathedral from the 1590s on, it would have certainly been larger (not a single structure but a sort of complex, most likely) and inclusive of more local influences because of the difficulty of quarrying the requisite stone. So it had the form of a small church, but I suspect a much more visibly syncretic element would have been the entire site taken together, as such complexes were. There's just no clear information about it.]