Well, I'm going to spit-ball for a second. Perhaps, given the aerodynamic efficiencies of the P-51D are mainly efficiencies created by lower parasitic drag, that at high altitudes, where parasitic drag makes up less of the overall drag, and where induced drag makes up more of the overall drag, the Pony will enjoy a smaller speed advantage. At sea level, where more of the drag is parasitic, we see a larger discrepancies in the two top speeds. Assuming both the Spit 9 and Pony are making the same amount of thrust at all altitudes, the lower parasitic drag of the Pony would enable it to be even faster at sea level than it would at altitude.
This is a simplified example, but I believe it is probably what a more detailed analysis would reveal. Ultimately, its the ability for the Pony to make full rated horsepower up to a very high critical altitude that gives it its excellent high altitude performance, not unlike its peer the P-47, which certainly did not earn its high-altitude performance from being dainty.