Let me reword this without using the term "VE", since that seems to be distracting you.

Revisit your conditions again: same engine, same amount of boost and same temperature in the intake manifold.

The conditions in the intake manifold are exactly the same between both setups, and both are using the same exact engine.

The engines themselves are identical in how efficiently they can consume air.

Please explain to me how one engine can consume more air from the intake manifold than the other, given that the engines are the same, and conditions in the intake manifold are the same.

The engine does not care WHAT created the conditions in the intake manifold, or HOW the conditions were created. It just consumes air from the intake manifold.