Why should it be free?

Because it is necessary for a functioning device. Because they made changes to their charger during that generation for improved performance. "Free" is a loaded term in this context. It should be included in the purchase.

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.

This attitude leads to mountains of e-waste. No thanks.

But yeah drop the user guide too and put it on a website, good idea. The box, not that because it protects the product leading to less wastage.

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.

I don’t know what to say apart from this is cynical.

If people are going to buy consumer goods anyone trying to make it a bit better should be celebrated.