That's not the take. It's that this is very expensive. And one of the top upgrades is optional as opposed to included. The point is that a $49 accessory should be included in the box on a $1,799 phone. That's reasonable.
Also, it's great that the charger is available through Samsung, but most people don't buy through them. They go through carriers or other retailers.
How is that not the take? Including the Pen would increase the price and not everyone will want or need the pen. I think they'd appreciate not being forced to pay more for something that they don't want. Just because something is expensive doesn't mean that people should be given other products for free.