It is a wandering and unpredictable piece, and the structure is hard to parse as well.
I think that Baptiste had trouble transcribing a scale that included microtones he was not familiar with The scale is an eight-note scale, not including the octave, which is an unusual occurrence in both Western and African musics. Two of the notes are a semitone apart (adjacent keys on the keyboard), with one of the notes designated as the keynote, which makes for an even stranger structure. I'll just copy from the 1993 article. Sorry for the self-reference, but it addresses this directly:
The first two sections of "Koromanti" use seven notes, the third, eight. The extra note in the third section was probably the result of an attempt by Baptiste to record microtones, which cannot be represented by stan- dard European notation. Many African (as well as other) musical traditions make use of microtones in their tunings. These are notes somewhere between the European semitones; on a piano, they would fall between the keys. An example familiar to Western audiences (albeit one of African ancestry) would be the bending of a string by a blues or rock guitar player to accent a note. Microtones are perceived by the Western ear, accultur- ated to tempered tuning, as being out of tune.
The microtonal section of "Koromanti" has both G and Q, which is highly unlikely because the section uses G as its root note (the fourth mode of the tonality of D major, which the third section is in, begins on G). More likely, the fourth is raised, so that it lies somewhere between a European G and G#. Baptiste probably did not know how to deal with this and rendered some of the notes as G and others as G#. Correction would give a third heptatonic scale for the piece, as the eight notes would then become seven,kith the third and seventh notes partially flatted (Table II).
The use of microtones is not common among the Akan, who show a preference for a heptatonic scale based on the natural overtone series that is equivalent to a nontempered version of a European major scale, where the seventh interval is flatted slightly. This type of scale would not have caused Baptiste any confusion. The Angola region, which is known for its employment of microtones, is not known for its use of heptatonic scales. Although "Koromanti" contains several traditional Akan melodic struc- tures. the musician used these features in unconventional ways."
The upshot of all this is that it fits neatly in none of the boxes here: West African, Central African, European. Nonetheless, it is an immediately recognizable sound as the blues scale originating in African American music, with its microtonally flatted third and seventh (and sometimes fifth): aka the blue notes found in everything from blues and jazz to the horn sections in reggae. The scale in other words is no longer locateable in the traditions that make it up, but is creolized. To me, the fact that Baptiste had so much trouble with this points toward him not being a creole listener. Setting the microtones right yields a D Blues scale with seven notes. The piece then coheres much better. I can provide musical examples, though not as nice as the "Passages" recordings!