Lets make it easy for ourselves. My system for adjusting my camera/lens combination, for use on my superb NN180, is very simple. I set up the tripod and camera so that they are level. I then choose my near and far reference points, adjust the camera position and finally check to make sure everything is still level. Business as usual. Here is where I simplify matters: I line up my two reference points in the dead centre of the viewfinder and then pan to the extreme left or right (it doesn't matter which) edge. It is now that I adjust my camera on the rail until the two reference points are aligned again. A quick pan over to the other side to check for movement and hey presto, all is done. Once the camera is setup on the tripod, 30 seconds will do it, including tightening the screws. It is so quick and easy, it makes it simple to do on the fly with different lenses.
That's fine for standard rectilinear lenses but not fisheyes. Your method aligns the entrance pupil with the axis of rotation. The problem is that a fisheye lens doesn't have an entrance pupil located at a single point. Its apparent position varies for light rays entering the lens at different angles to the optical axis. This means you need to check for parallax at the angle where the images will be joined. E.g. if you are taking a full 360 pano with three shots (yaw increment 120), then check for parallax at +/-60 degrees to the straight ahead position rather than at the extreme edges, which might be at 90 degrees.
Not having a fisheye lens, I welcome your input but, for rectilinear lenses, my method seems a lot easier than keep returning to the straight ahead position to adjust after checking for parallax at the edges.