please correct me if I'm wrong.
Compare your results to mine and decide for yourself.
There are many factors in making proper mipmaps.
#1: A proper and sharp filter, such as a Kaiser filter. Judging by your first mipmap, Paint.NET uses a pretty crappy down-sampling filter. I judge based only on the first mipmap because you can’t make mistake #2 with it, which is-
#2: Every mipmap level must be calculated from the original full-sized image. It is a mistake to halve the image, then halve that image, then halve that image etc. down to 1×1. Halve the main image. Then fourth it. Then eighth it.
#3: Premultiply alpha before generating the mipmaps. But you are already doing this.
There is no real solution to on-screen positions. Your focus should only be on the mipmap quality. Use my image and check the result.
L. Spiro