If changes are made to the steering components, the sensors are supposed to be recalibrated afterwards. You are absolutely right in your theory that the one Spyder was so far out of whack the sensors thought it was bad after the realignment, and put it into limp mode. There is a small amount of deadband (since the first steering recall back in 2009 or 2010), but changes outside that deadband would cause immediate limp mode. Even if the changes are within the deadband, the Spyder can go into limp mode after a long mismatch, like side winds or long sweeping curves, or it can pull to one side and even wear down a brake pad, as the VSS tries to "correct" the steering. Zeroing the steering sensors on BUDS is highly recommended after any alignment work or suspension changes.
The Spyder doesn't like the high banks, especially at relatively low speeds (< 100) because of the yaw sensor. It thinks the Spyder is unstable and triggers the VSS "Save Your Butt" mode.