I made that diagram to show that the liner is not structural in nature. The gap that you say is present would not be a structural issue to me. It is however a way for water to get into the bilge so you may want to seal it. I have seen these boats with this gap filled with putty but due to the natural flexing of the hullsides there are usually cracks that form. You could pull back the carpet,grind,and glass the seam or fill with a flexible caulking.
