inkscape can mesure the objects using the “visual” or “geometrical” bounding box. (menu edit / preferences / tools)
the first option adds the stroke width, so the size changes if you change the stroke (but not the nodes).
the second take only in account the nodes, and ignores the stroke width.
as LB as no “width” on the stroke, to get accurate result the best way is to setup inkscape to use the geometrical bounding box.