Usually these kinds of things have unforseen "ripple" effects. Therefore avoiding any significant modifications saves you more trouble down the line.
Don't try heal to solve it- it will just lead to warpage.
Don's idea is a good one, it's commonly used in aircraft modeling to get the fuselage to fill the gap between the wings.
I have never built that kit, but I also have not heard of that problem in a brief search through reviews on the www. Double check and be sure you have the assembly right. Maybe the deck is supposed to sit on top of the hull. That ship DOES have a funny looking connection there, sort of a step.
Just my two bits.