Hey, just be happy you got layers.
That alone would make me happy.
Though, truth be told, the PS files I deal with are so large when flat, I’m usually just fine with that unless there are logos to color correct (missing smart objects).
Illustrator and Indesign on the other hand…If you put your die-line and white layer in, then flatten it to one layer, that is irksome. I can deal with Layer 1, Layer 2, etc, as long as everything is on the correct layer.
I particularly love when elements drop out because the designer put something that was supposed to print onto one of the non-printing layers. Somehow that’s supposed to be my fault?
Mine are totally organized like the one on top. pffft, yeah right.
They should be at least close to that. For your own sake.