Slide weight, and ammo and spring.
The .40 P99 uses the same recoil spring as the 9mm P99. They made to slide heavier to compensate for the more powerful round. This pistol will probably never be as inherently reliable as a 9mm pistol with this barrel (being heavier than even the .40 barrel), with the slide being heavier than the 9mm slide, and with the extractor, ejector, and breechface not being the optimal size, shape, and in the optimal placement and position for the 9mm round.
I'd imagine that if the manufacturers of these pistols could make pistols that were just as reliable with just a barrel swap and magazines, that there wouldn't be anymore design differences for the 9mm and .40 models.