i notice that overprint in stroke is always calculated from center of the stroke and ignores the stroke alignment setting(Align Stroke: Center/Inside/Outside).
See following screenshot, in the 3 objects, all Fill size = 100x100 pt and Stroke size = 10x10 pt, the only difference is that Align Stroke setting, from left to right: Align Stroke to Inside, Align Stoke to Center, Align Stroke to Outside, you will see the overprinting result.
Is that a problem? or i miss something?