During this throttle, I would get whiteish grey smoke, looking like unburnt diesel to me. Would this be from the engine getting so cool? EGT's were reading 0.
Your diagnosis sounds pretty likely to me. The pump governor will cut off fuel completely on overrun, so your momentary applications of throttle would be effectively restarting the cool engine without glow plugs and at a high altitude to boot, sort of a worst case scenario. You would expect to see some start-up smoke under these conditions. I doubt anything is wrong.
(Edit) Another cause of smoke could be the turbo. Under no-boost conditions there is really nothing to prevent oil from leaking into the compressor housing, there are really no "seals" in the turbo, just mechanical flingers or labrynths. Without positive pressure in the compressor some oil can make its way into the housing and burn off when you gas it again. Again, not really a problem, just a condition unique to your very long low power run. If the exhaust smelled strongly of oil then this would be the likely cause.