I can see simplicity reasons to sell the user guide and box separately, too. Why not just hand them $1k in cash and get an unboxed phone? Much simpler than packaging and credit cards.
The means by which people will bend over backwards to paint Apple in a good light is insane.
It is trivial to reduce the environmental impact by changing the type of packaging materials and shipping multiple phones in one carton, while protecting each phone individually. Apple chooses not to do this since it doesn't fit their marketing strategy.
As for those missing chargers, they probably have multiple reasons for not including them. The environmental impact may even play a small role. Ultimately though, the main reasons are going to be business driven (e.g. reduced manufacturing costs and perhaps increased sales of chargers). If these people were truly interested in protecting the environment, they wouldn't be in the business of selling disposable consumer goods.
If you need one, buy one.
I don’t see any practical, technical, ethical reason to include one. I see environmental and simplicity reasons to not include one.