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From what I can tell on my car, the air entering at the base of the windshield doesn't ever enter the engine bay... it either enters through the cabin (if you have the vents open, fan on, and recirc off) or it doesn't enter at all (if you have vents closed, fan off, recirc on).
It would make sense to have the air going into the cabin separate from the air going through the engine compartment, since the smells from the engine compartment (not to mention the potentially dangerous exhaust) would not be pleasant in the cabin.
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