I honestly have no idea where the shiny female sprites came from then, because as you've shown, they arent in the base game (also I didn't have them before), and yet the only thing Ive copied in is your texture pack, but I just checked my original zip i copied from and they arent there either...
I think it would be cool to try something for the box sprites, because they do look somewhat out of place, but if it doesn't look good I guess don't worry too much? Because you're distributing the texturepack not the program, could you just make the changes, rerun for the gen 6 box sprites and replace those if you dont wanna mess with any others.