Back when I had my 00 TJ sahara, it was automatically registered as a truck. My Liberty was automatically considered a wagon! haha
I would just say go for the truck if you have the option. It isn't going to save you that much money to register as a car, the bigger difference is year, and it will likely eliminate that legal question if need be. I also don't think you'll have an issue, but if you're worried about the law, go ask your local PD, they will certainly tell you what they look for!
06 LJ RUBI, with stuff, and more stuff planned :)