This will get submitted as a bug, but I believe it warrants discussion.

1) It seems the ruler co-ordiante system is flipped in the y-axis w.r.t. the SVG co-ordinate system.

The rulers have their origin on the bottom left of the given viewport, and the co-ordinates increase up and to the right. This goes against the SVG spec, which states that the origin of the viewport is on the top left, and co-ordinates increase to the right and down. When creating a rectangle and manually specifying the (x,y) = (0,0), the top left corner is placed at the top left of the viewport.

Odd that nobody noticed this earlier.

2) The markings used in the ruler gradations aren't anti-aliased. It looks like Inkscape uses some sort of customized GTK ruler.

One should note that the GTKRuler class is being moved out of GTK+ because it's too specialized/little-used. One would think that just about any drawing/display app needing co-ordinates in its display canvas would use them.