I don't understand why your model would look "weird" or why gutter location has anything to do with dimensioning?
Well, I'll try to explain it as quickly as possible. In order to correctly layout your cornice/entableture the top of the gutter needs to be aligned with the top of the fascia. The distance from the frieze board to the outside of the gutter (In this case ~8-9") must equal the distance from the top of the fascia to the bottom of the bed mold.
If I can't move the gutter up to the top of the fascia in my model, then it won't match the details. I know in the world of construction details are the driving factor not the elevations however, the architect that reviews my plans for this neighborhood is a STICKLER for detail, regardless of weather it's an actual detail, or the elevation.
So I'd prefer to be able to make my model match what's in my details. But Softplan makes that difficult in that I can't move the gutter, and adding bed mold under my soffit is a huge pain in the arse.
It should look like this when your done: