I think it's that he gets the founder belief of the majority religion in his empire.
I think this is wrong and I am not sure if anybody in this thread has it right. The narrator says "he does get the Founder Beliefs of any religion that has established itself in the majority of his cities". This clearly means that he can have Founders Beliefs from 2 and more religions. Actually, I think it is the most important part, otherwise his unique ability would in fact weaker him.
Example: Kongo has 5 cities, Catholicism coming from the west is in all of them (at least one follower), Buddhism coming from the east is in 3, and Judaism coming from the south is in two. So he gets Founders Beliefs from Catholicism and Buddhism, and needs to spread Judaism in to one more city to get it as well.
He probably gets those bonuses only in cities which actually do have 1 follower, so he should actively use religious units to spread those religions.
EDIT: Just realized that most of Founders Beliefs seem to require such religion to be majority religion in the city, which would mean Kongo can use only one in each city. But I think this has to work some other way. Collecting those Founder's Beliefs is the most important part, getting only one in each city would mean that his unique ability weakens him, which is nonsense. It would mean that in comparison to any other civ, he just loses tons of faith (no Holy Sites), Worship Beliefs and the right to choose its own Founders and Followers Beliefs, and gains in fact nothing for that.
EDIT2: Ok, seeing Denkt's post below me I have to admit that he gains something (by saving production on Holy Sites and future districts). But I still think/hope that he gets more of those beliefs, and wording in FL video supports that.