yeah I think what Just Blaze meant was that the basslines were dissonant, or out of key, with the samples they were under on some of the tracks.
the thing about music theory that I know misunderstood for a long time is, and I think there's a lot of confusion over, is the whole idea that there are "rules" in music theory. there aren't really any rules. music theory was first being studied and approached from the perspective on church hymns and european classical music, and usually if you take a piano class or a theory class they start you off studying classical music. a lot of people end up making the mistake thinking that the way european classical music is written is what music theory is... not the case.
that early classical and church music was concerned with the most "pleasing" and "agreeable" combinations of notes.
Other styles of music, like jazz for example, work with more "tense" combinations of notes.
Then there's styles of music that are more experimental that work with dissonance, combinations of notes that purposely clash and sound "off"
Music theory has something to say about all of it, so learning theory wouldn't necessarily make you say it's wrong.. you'd just know it was dissonant.