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However, since the runway and air molecules are relative to one another

My point was that they're NOT. If the runway is a conveyor belt, it's moving independently of the air molecules.

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in order for the plane to move across the molecules it would have to also move across the runway.

Not if the runway (conveyor belt) moves independently of the air molecules. Depending on how you interpret the question, the runway is either moving the same direction of the plane's travel, or opposite the plane's travel, but either way, it's independent of the air. The plane is either not moving with relation to the runway/belt, or moving twice as fast with relation to the runway/belt, but again, that's completely independent of its real-world (relative to the air) motion.

I know we're just arguing semantics. I just didn't make clear that the plane really DOES move.
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Tony Fabris