Yesterday I did some research on the differences between a UT Save file and .pkm file and a Pokesav touched one.
It appears that when using Pokesav, if you simply load a Save file into pokesav and save it without making any changes, the coding does change to leave possible traces.
Though it seems that for .pkm files there is no difference in a normal game generated pokemon and a pokesav/pokegen generated one.
I have checked this by looking at the hex information and comparing it to edited information, for example:
I used a game generated legit starly and copied it. The copy was then loaded into Pokesav and saved (it is identical LOOKING in everyway to the original), then I took the two and compared them in hXd and they were identical. I did the same with loading it into Pokegen and then saving, it was still identical to the legit one in everyway possible.
I then took a legit save file and copied it 3 times, and loaded each one into either Pokesav, Pokegen, or PPSE and saved. However, when comparing them to the original one this time there were differences (small differences for Pokesav(easily fixable), larger for Pokegen, and VERY large hex difference with PPSE).
I have not tested ARDS yet but plan to soon.