@33coupe They say they can't use a straight pipe since it's not centered to the lower gutter, so my question would be was it meant to be centered? What does it look like on the plans?
I suspect it was meant to be centered with a straight pipe and someone screwed up so they added the spreader is the cheapest "fix" available. Looking at your plans should verify if that's correct or not. If it was meant to be centered then that's defective workmanship and on them to fix if it bothers you (unless you signed off on a change during the build). If it's like that on the plan that you signed off on then you'll need to foot the bill for any modifications.
I'm curious about the different soffit heights, do you have a mix of different internal ceiling heights?