@Alexander @chenyuzhou I think I found a solution.

As Nate recommended, I used GIMP to do the scaling of the atlas texture page. The key was to set the Quality: Interpolation to None:

The default is Cubic, but that did not work because it added extra processing to the transparent pixels when scaled.

Then select File - Export As... and enable Save color values from transparent pixels in the export options. (This is as shown in the video introduced by Nate):

Then changing the image path of the skeleton to refer to the unpacked images should result in the look of the first image shown.
I hope this helps you.