Having tested in VR, it works correctly and the same as 2d, the pilots seat in the ship and the HUD are aiming at the central rotation point of the ship off into the horizon (or infinity. Or the skybox). In effect you are looking slightly inward at a point on the horizon, the same point where if you were sitting in the middle you'd be looking at. I can show it in VR.
I started the recording in the seat, put the mouse widget on. Moved the ship so it was aiming exactly at a star, the mouse widget on the star. The mouse widget is fakery, but it works to mark a star and see if we roll exactly on that axis. Flight assist off, started a slow roll. The ship from the seated position rolls perfectly on that dot, as in 2d. Stand up, move left to the centre of the ship (the video jumps as I pressed the recenter view button just so I could move left without falling out my window
) and you can see it's perfectly aligned with the roll, the dot on the star. Moving far left and far right without recentering and you can see the ship is rolling the way you think you should be seeing, ie the other side of the cockpit moving much more than the centre, but you aren't taking in to account the hud and seat are pointing correctly at the actual point on the skybox where the ship is pointing and rotating, marked by the mouse widget. You're thinking the hud and cockpit should be pointing parallel to it I think. Also - the ship is HUGE in length, and the seat is only like 2 feet offset from the centre. Your image with the red and green circles you're expecting to see the rotation at the green circle which is just under the window, but the ship goes so far out in front! In fact, the nose is out pointing where your red circle is, the cockpit up really high above the long nose that slopes down out of sight. It's correct.
In VR it really is clear the ship IS rotating around it's centre axis. Because where I'm looking (in VR) is irrelevant to what the ship is doing. In 2d it doesn't seem that way, but it genuinely is.
I don't have youtube to upload, here's the video:
Source: https://imgur.com/99XERkv