The stiffener is flexible enough that the transition from the next forward rivet (stiffener to side skin) to the aft-most rivet where the aft bottom skin is sandwiched between the side skin and stiffener is not noticeable from the outside. Once you rivet it, you will see there is plenty of strength there despite the fact that the side skin is not fully in contact with the stiffener for a short distance. If it really bothered you, you could form a joggle there but it should be fine as is.
There will be other places where the fit is not perfect. For some reason, the overlap of the inboard/outboard wing skins where they meet the leading edge leaps to mind. I beveled mine to make a better fit but I've seen plenty that did not bother. I'm probably misquoting "Perfection is the enemy of good enough", but, really, these kits are fine as designed.
Patrick Kelley - Flagstaff, AZ
RV-6A N156PK - Flying too much to paint
RV-10 14MX(reserved) - Fuselage on gear
EAA Technical Counselor #5357