While it definitely sounds like you know a shade more than me on the subject, my experience with a DR650 at altitude was good.
We took 3 of them along the Pamir at up to 4600m, and were at least a week above 4000m. The two totally stock bikes idled and ran fine, but essentially had nothing beyond half throttle. We could just get them up to 100km/h. Riding slower gave no issues though.
One bike had a Staintune exhaust, stock airbox and unknown carb internals. It had zero issues, could pull to 100, and ran like normal... or possibly my girlfriend just never uses beyond half throttle anyway...
Ben
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Vladivostok - Denmark 2008... Finished.
Denmark - South Africa 2010-2011... Finished.
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