@NathanKell
Okay, the issue is not as straightforward as I believed, but still, the problem has to do with the fact that velocities/trajectories are not using the same reference point as angular momentum, which should be the CoM.
I ran some tests with the following rig (the weird radial decoupler thing was just to rule out staging as a cause), and regardless of what I would do, velocities and trajectories were always calculated relative to the bottom lander pod. The vessel was rotating from its CoM, the controlled part was the middle pod, yet when I built up a decent amount of yaw momentum, I could clearly see the surface velocity varying according the bottom pod's movement; when the bottom pod was rotating in prograde direction, the surf vel increased, and when it was rotating in retrograde direction, the surf vel decreased. If I removed the top and bottom pods, then the velocity was roughly relative to the bottommost girder segment that was right above the bottom pod... And, as expected, if I removed everything but the middle pod, then all worked fine and the surf vel didn't change on rotation.
So, there's definitely something wacky happening here. The velocities roughly appear to be relative to either the bottommost or outermost part, regardless of any other variable.