.5px mistake will take place not only for 1px wide shapes but for 3, 5 and any odd width. And there is no mistake on even widths.
.5 px drawing/scaling step may be only possible salvation. I have meet such solution in opengl based software.
But I think it should be not manual shift but burned into program code. Other way we may get even more ugliness.
This is common problem for pixel-based vector editor like SCADA-systems and so on - how to treat coordinate and width itself
What is the X and Y - coordinates? Is it border between pixels or is it center of pixel. Paint.net answer - it is border, but i have meet center-based software.
As result paint net smoothed 1,3,5,... pixel width lines, other software smoothed 2,4,6,... pixel lines...
Btw. Meet some other width-treating example in paint.net...
For example, 14x14 rectangle will have same external size no matter what width is their lines. Any other figures increase their external size with line width increasing.
So we have different treat for width for rectangle and any other figures in paint.net.