Drawing a straight vertical line segment with a pen (holding shift) will show a width of 1px and a width of 1cm and a width of 1in. Changing the width, for example to 2in makes the line diagonal. Returning it to 1in makes the line less diagonal but not straight.
The pen tool shouldn't use the bitmap coordinates to say the line has a width, that's what the stroke is for. A straight vertical line should have a width of zero, a straight horizontal line should have a height of zero. These are correctly points in the mathematical sense.
Is something not working like it should? Let us know.