The following interviews with the creators of Kult confirm a lot of things: The original three creators (of first edition) wanted different things. Two of them wanted an occult game, while the third one wanted a supernatural spy game, and they felt like they completed eachother's visions somehow. They were also the creators of The Black Madonna.

Then, with fourth edition, Petter Nallo almost rebuilt the world from scratch, just focusing on the personal horror elements, and trying to make the world make more metaphysical sense. He agrees that The Black Madonna doesn't really fit the 4th edition setting, and so I shouldn't judge the game by this module.

These interviews answer all my questions. =)