It may be the limitation is not due to the airframe or the engine, but to the oxygen equipment fitted. Above 39,000 ft pilots' oxygen masks need a positive pressure breathing facility, below 39k they don't.
Quite a few military aircraft were limited in this way. I can't find the exact spec for the equipment Airbus use - I believe EROS supply it - so if anyone has any technical links I'd be grateful. The FCOMs aren't detailed enough.