I do plan on allowing the origin to be moved. It isn't in the next set of changes to be made but it isn't too far off.
The reason rectangle coordinates are from the corner facing the origin is because that is the CAD standard. It is much easier to measure to a corner of a rectangle physically than to the center of the rectangle.
Resizable corner radii on the rectangles would be very nice and I will add that to the list of enhancements.
The paths can be resized by drag-editing. If you hover over a corner you can drag it. I intend to enhance this soon and add numerical entry for an additional method of editing paths.
Do you have a good idea of a minimum size to be allowed? I can't allow 0, so I need a slightly larger than 0 value.
I will look into the issue of always keeping the coordinates of the cutouts the same after resizing.
Thank you for your feedback!