i know when shipped long distance many detune/loosen the strings to relief tension from the neck, so maybe they just didnt tune it for that reason and just put your springs in the case....
i mostly buy used and specifically look after this possible issue. and never had one that had its neck shifted in transport.
of course its more tragic if a neck thru has this problem and i`ve seen many
maybe an cnc calibration problem on this particular model where the neck joint is cut unprecisely
if you shift the neck be careful not to cause any cracks