reference plane of wall construction with differnet wall thickness

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E+ doesn't really "refer t other middle of the wall" it is doing 2d not 3d calculations. There are common modeling practices for interior walls to be draw to the middle of the thickness, but exterior walls are generally drawn to the outside of the wall, not the middle. This represents the exterior exposed area well despite, but of course over estimate the floor area a little. A user can override the auto-calculated floor area but that generally isn't done. I feel floors and ceilings generally don't follow the same rule. Most people draw floors at the top of the finished floor, and then windows heights are set above that. They care more about the window sill height to floor related to daylighting than the proper position of the floor relative to the actual building height.

You could adjust your geometry have the thicker wall sit out, but I wouldn't worry about it; the exception might be if you have a large window next to the green wall that's sun exposure may be impacted by your green wall. You can't just step out the facade, because then you have two additional segments that you don't intended to so you would have to have what appears to be gaps in the wall where it steps out, and might have to manually calculate the floor area and volume .