I'm with you now Jake (sorry for my previous irrelevant rambling)
The altitude will not really affect your muzzle velocity, but the air temperature difference might affect it if you're using a powder that's sensitive to ambient temperature.
The bullet will retain velocity much better at high altitude, and MOBALL certainly does account for that affect on the bullets flight.
The only program that I know of that accounts for the effects of temperature on muzzle velocity is Load Base. I don't know of any that account for altitude effect on MV because frankly, altitude itself doesn't affect MV.
I hope I answered your question this time