The retail price you set during production is often the same as the cover price or selling price retailers use, but it doesn't have to be, and that is up to the retailer, not you, and not us.
When you set the retail price for your book, you are setting a suggested retail price. All retailers have the option of selling your book for whatever price they want (or not selling it at all). If their list price is lower than your suggested retail price, the retailer is absorbing the difference in their portion of the margin.
Regardless of the final sell price, you still earn the full royalty amount that you set during the pricing phase.