Could be because humans tend to veer towards just intonation rather than well tempered intonation in the absence of frets, keys, and other mechanical factors corralling them into true tempered. Apparently just intonation is what the human ear and brain, if left to themselves, prefer over the stretched intervals we learn to accept as “correct” in Western music.
A cappella vocal ensembles and scale free instruments (such as strings) will often shift to just intonation when not playing with fixed pitch instruments.
I wouldn’t be surprised if he was playing with just intonation.
I understand where he is going harmonically, and in a lot of the chordal work the intonation is right on the mark. But the single note lines are not pitched quite bright enough for me. There's hardly anything in it, and I do understand the amount of hours it takes to get to that level, I certainly don't expect 'perfect' intonation all of the way for sure. I think it would be much better, with a static reference. Lines.