Because then if I want to add a new character I need to re-export every single texture I've ever used in my project.
If I have subdirectories..
Apple
Orange
Zebra
I get Atlas.png Atlas1.png Atlas2.png
(Apple, Orange, Zebra, respectively)
and I add a new one called TexturePackerIsDumb
I get Atlas.png Atlas1.png Atlas2.png Atlas3.png
(Apple, Orange, TexturePackerIsDumb, Zebra, respectively)
and all my assets that are already packed in my deployed projects are now questionably linked to their original texture if I ever need to delta patch anything.