Why not mount those low-profile thumb wheels inside the f-holes? You could just drill a tiny hole under the pickup to run the wire. You could mount them with double-sided foam tape.
Here is a Mark Campellone that has thumbwheels only (look very closely at the treble f-hole)
You could also find an old DeArmond control box which is exactly what you describe but they are rare and pricey. I would rather have the thumb wheels. Less effect on the acoustic sound.
Didn't vega guitars have a tailpiece-mounted control scheme?
Edit: yup.
Vega Duotron