The reason for the short delay is Apple wanted to provide consumers with the absolute best product imaginable. As others have said, they have re-engineered the packaging to alter the contents to improve the overall out-of-box experience. This will have cost Apple both time and money. No other company would do this for customers.
I am confident Apple will be getting pencils into the hands of the majority of customers who want them by the end of the week.
Are you trying to say the delay was to add the charging adapter? Because if that's the case it doesn't really paint a better picture (suggesting that they only knew it needed that adapter after the complaints online).