yes, the trailer box will shift the COG and overall weight a bit.
After knowing the total all-up weight, can you just fiddle with the axle position using the weight on the tongue? Did you say 10% of the total weight should be at the hitch?
I recall first using the N20 trailer (without a sailbox) and the boat was about 1 foot too far back. There was very little weight on the tongue and it jiggled up at almost every bump.
Kind of spooky now, thinking that it could have popped off while trailering it down I-10. But ignorance is bliss... (until the trailer pops off)
10% of the overall trailer weight on the tongue is the general rule. I like to run a little more than that when possible.