Due to the huge surface area and the rocker in the Gemini, I don't think I'd try going down the road at speed with the board standing on it's side. I think you might break your rack doing this.
How long is your trailer?
I'd think you could build a "top rack" on the trailer to get the Gemini up above everything else.
If you have to put the kayak on the trailer and keep the Gemini flat on the roof so be it.
Even if the Gemini hangs off the back of the trailer a bit, hang a red flag from the rear fin screw hole and I think you'd be OK.