On my previous computer, I remember changing a setting in Inkscape so that an object's coordinates are independent of the width of its stroke, and remain the same when it is changed (i.e. the coordinates of, say, a rectangle refer to its control points, not to its physical bounding box).
I am now on a new computer with a fresh install of Inkscape, and do not remember how I changed this at the time. I've been through the entirety of the Document Properties and Preferences dialogs, but can't seem to find it there. Google has unfortunately been no help either.