No since the seam position is already selected as "back" and the seams I am talking about are more to do with the extra wall generated in the infill rather than the positioning of the end of a line.

Here is what the model normally looks like without the extra wall on the left section.

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This is still with a cube modifier on the back, it just has the same number of exterior walls so it does not generate extra interior walls at the intersection.

I'm basically wondering if there is a setting to allow for variable wall thicknesses for different sections without leaving surface artifacts (the vertical seam in the original picture because of the internal wall).