Inkscape includes the border width in the displayed object size and position. So an SVG file with a 100 units square and a 1 unit border will be a 101 units squ

Inkscape includes the border width in the displayed object size and position. So an SVG file with a 100 units square and a 1 unit border will be a 101 units square in Inkscape. And if you change the stroke width the object size changes. This causes the coordinate mangling you saw. Consequently, I find it impossible to do precise CAD style diagrams in Inkscape. Of course, it's not designed for that.