Not using Paint.NET.
However, here are some alternatives:
In explorer, right-click Preview an image in one window, open the other in Paint.NET. Arrange the windows side-by-side.
Or, if all you REALLY want to do is compare images, open each on a different layer, change the top layer's blending mode to XOR. Where the images are the same it will show black, where they differ it will show color.
Hope this helps.