Whilst I have no doubt that normal operations have never exceeded 45,100 feet, it must be remembered that for every published operating limit, certification and test flying must go beyond the nominated limit to ascertain the margins. This applies in all areas, Vmo, Mmo etc. (To be more exact, testing goes to 'the limit', and a margin then applied to establish a lower 'normal' limit).
Would you fly an aircraft to the published limits, in the knowledge that the test pilots had never evaluated the aircraft one foot of altitude or one knot of speed beyond the limits you're using?
So, whilst 'regular' operations may have never exceeded 45,100 feet, Boeing would have tested the aircraft, both the aerodynamics and the systems, to a Pressure Height somewhat beyond that. 747Focal might be able to shed some light on this.
In some aircraft that I did test flying for in an earlier life, 4,000 feet above was not out of the ordinary.
Regards,
Old Smokey