Ok I see where you’re coming from. Martin seems like he knows “everything”, so naturally we assume that this is what is required to work through his process. It’s not - it is the result of it.
When you watch this conversation, it’s hard to parse out the things Martin knows and where they all came from. But if you notice, once we start working out the II-V-I lines, we’re talking mostly about scale shapes, scale degrees, and the sound of chord tones – all things that can be learned by playing and listening. What is cool is watching him learn, on the spot, in the talk. He plays a line, decides it sounds weird, and tries another variation on it, until he gets one he likes that ends on the right chord tone. This is the process you run through to become familiar with the sound of each scale degree, the sound of hitting the chord tones at just the right moment in metric time, and so on. The more you do this, the more you learn things like, ah, ok, I’m hitting the third of the chord on the downbeat. You end up with a strong practical understanding of the relationships between things. But you are building that knowledge in a natural, hands-on way, by trying and listening. It’s cool.
To begin this process, the core “harmony” knowledge you start out with, is super simple, big picture kind of stuff: what a particular chord sounds like, and what scale notes you’d use to play over it. In this case, we’re using some jazzy sounds like the altered scale, which you don’t see often in rock. It probably makes things sound a little more complicated than they are, particularly when he starts saying he likes certain notes in that scale, like the flat 9, or the sharp 9. But again, those preferences are developed by running through the process itself, not as a book learning “homework”-type process that happens beforehand. This talk could just as easily have been done with the vanilla major scale, or something else simple that everyone would be more familiar with.