Bingo. I've personally had to deal with this in other high-density systems. Less cooling not only has the obvious effects, but also reduces PS efficiency which can cause other problems. Cosmic-ray-induced memory errors can also be a problem at those altitudes (or even half that). That's a bit easier to deal with in principle, but the rate of ECC scrubbing required can start to impact performance. Stack that on top of thermal CPU throttling, and you'll have a system that's just slower than it should be. Just as importantly, the slowdown will be uneven across components, so it's effectively a different kind of system when you're debugging low-level issues.

I think it's a good sign that they're aware of the additional support issues associated with higher altitude. Shows that they've really thought things through.