Assuming that you have encountered an offer that includes an Apple Pencil, the purchase invoice will include the retail cost of the Apple Pencil - however, the iPad cost will have been reduced by the same amount.
As such, you have not been disadvantaged - as the total invoice cost, that has been charged to your Credit Card, will still be no more that the original cost-price of the iPad prior to the equivalent discount being applied. Effectively, you have both a new iPad and Apple Pencil for the cost of the iPad alone.
Apple invoices in this manner to avoid potential fraud - where a new iPad is subsequently returned for full refund without also returning the Pencil.