You dont understand core of the problem. (please do excuse me Im not trying to be rude, EN is not my native language - I dont know how to express that sentence without being rude, but be sure that I dont have that intention)
Problem is happening to files that ware created outside of Paint.net. In test image, I provided in zip file, in my first post - you can observe bug happening.
-First open native file in PS or Gimp and see resolution - 72
-Than open in Paint.net and check there - 96
-Than save image in Paint.net without resizing it or doing anything - just "save as" a backup png copy
-finally open copy in PS/Gimp and copy resolution would be 96
From observation above - you can see that PS is displaying true resolution of native file whichever it may be 72 or 96, but Paint.net is changing resolution of native file to 96 without any notice.
I dont know in which program that png file is created. It may be Paint.net issue only with that kind of PNG, but it is still an issue, since PS or other programs dont do that automatic change of native file.
I hope that issue is now more clear.