There's more to eco friendly packaging than just the environmental impact of said package production. If you can fit more product in a crate because it takes up less space and is lighter, the energy costs of going from point A to B are reduced.
I can be critical of Apple with very little effort (lol), but this doesn't seem like one of those things to be upset about. Fancy packaging is not necessary, and most of it ends up straight in a landfill, I am sure. We should see less packaging from commercial products globally, not more. Whether this saves Apple money isn't terribly relevant to me. Less waste is always going to be the better way to do things.
Having said that, the yearly upgrade cycle on these devices is what I am most critical of. Encouraging people to consume as often as possible is a huge stain on environmental impact scores.