The full length body pan is unquestionably the better option. And vortex generators on the subframe will do little.
However, here's something you can try. If you've got a smooth pan under the nose of your front end, and it extends back to/under the engine compartment, and it's LOWER THAN THE SUBFRAME (and anything else in the area), you can place some VG's at the trailing edge of the pan to energize the airflow under the car. It doesn't keep air totally away from the rough surface of the underbody, but it will provide some deflection at speed.
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