The GPS was not showing the aircraft's altitude. It was showing the receiver's height above the WGS84 ellipsoid - a theoretical model of the earth. The pilot may have announced the aircraft's altitude as 41000ft, but it was not. It would have been Flight Level 410, which is 41,000ft above a standard pressure level of 1013.2 HPa - a nicety that most passengers are unaware of, and it's not really important (to the passengers) anyway.
Sorry, you can inform the author that he and his receiver aren't that clever!