Remember that the lungs are organs designed to rapidly exchange gas from the blood with the surrounding air. When you hold your breath the air within the lungs stays there, exchanging gas with the blood as you hold it. You can still absorb oxygen and expel carbon dioxide for a while, just less efficiently as the relative proportions begin to equalize.
But when you are exposed to high altitudes the air pressure is very low. This means the relative concentration of oxygen in the blood is much higher than in the thin air outside the body. The lungs then can act in reverse, rapidly dumping oxygen into the air! What this means is that your blood oxygen level will drop much faster than if you were holding your breath at normal air pressure.
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