It will NOT fit as tightly as it is designed to. On the correct vehicle, the Trail Cover is pretty good at keeping the elements out, especially with the doors off. If you are not taking the doors off, the difference in fit/function be less.
I am not sure how you started out this project, but both Bestop and Rugged Ridge make seat sliders which may work for your application. They do add a little height though. Call us at 877-553-5337 with any questions.