I suspect what’s happening is that your movement isn’t “strict” 903 wrist movement, but is some shade toward a “902” movement, with slight wrist extension at the end of downstrokes, and slight wrist flexion at the beginning of upstrokes. The pinky gliding along the pickguard “pushes” your wrist off of the strict 903 axis as you move through a downstroke. This is why your thumb can be closer to the guitar face at the end of a downstroke than the beginning of a downstroke, but your pinky remains at the same “height” above the guitar face both at the beginning of a downstroke and the end of a downstroke. In theory, you could accomplish the same thing through some sort of contortion of your palm or fingers, but that doesnt appear to be the case here. I guess the same result could also be accomplished with forearm rotation, but if there is any forearm rotation in your case, it’s very very subtle.
@adamprzezdziecki , I don’t know if my interpretation of @shinjuku 's picking helps shed any light on your picking for you. I guess one way to look at it is that if you can’t find a way to get strict 903 movement to have escaped upstrokes, maybe experimenting with something more 902-ish will be more palatable to you than adding forearm rotation. Looking at @shinjuku as an example, I’d say the more supinated your forearm posture is, the more a 903 action will tend to have escaped upstrokes, but also the more problematic the “where does my pinky go if not through the face of the guitar?” question becomes, and @shinjuku 's video shows one solution: the pinky slides along the guitar face, and the overall movement takes on a bit more of a “902” character.