I will offer a low tech explanation of the effect of altitude on performance.
A speed-density tuner, like the SEPST, TTS and Powervision will adjust to ambient conditions, i.e., lower atmospheric pressure. However, the air at altitude is less dense which requires less fuel. The tuner will adjust so the AFR is the same at altitude as it was at a lower altitude but there is less of it available for combustion at altitude. Combine that with the drop in CCP and the motor just doesn't have the guts that it has at lower altitude; smaller "boom" in the combustion chamber = loss in power. The upside is that fuel mileage will improve.
That is why you will not see 91 octane fuel in Denver; all 87 and 89 as the higher octane is not required. Comprende?
I have traveled from south Texas to Denver several times on both my EFI '05 Deuce and my '02 carbed FLHT. The EFI bike definitely exhibits a loss of power at altitude but the CV carbed FL is immune to altitude changes. I would never alter a tune to travel to altitude but if I moved to a higher altitude, say even from 600' where I am to the Texas panhandle at 3200', I would re-tune the EFI bike. The carbed bike could probably benefit from some ignition map tweaks, i.e., more timing but no fuel adjustments would be required.:s