Pre-clearing down there is one big FUK job right up the pooper shoot. I did it once and will NEVER do it again. Those dik-head customs folks love to go through every bag, they make sure you get dinged for duty on everything you may have bought. If you happen to be attempting to pre-clear during an airline push, you're really gonna get fuked. Could take you 2 hours.
You have to go over to the main terminal for this rape-session. They will not come over to the Gen-Av side.
And you are correct in that you cannot take advantage of the overflight exemption with none of the pax on board. The permit specifically states this.
However, if you have an excellent relationship with your local customs officer at your home base, give them a call and see if they'll give you relief. I have done this a couple of times.
Barring that, just shoot up to ILM and clear, never takes more than 15 minutes. But you've been warned about clearing in St. Thomas.
Good luck.