The difference in pricing depends on the taxes. Under Agency pricing, the base price is no different from retailer to retailer. How each retailer collects the taxes is differing and that is where you see the price differential.
How pricing is set today is actually dictated by Apple. Apple has required publishers to price based upon the physical retail price. So if the physical retail price is X, then the digital price is X.
From the Smashwords distribution email (and if you check the iBook pricing for digital books, it matches this pricing scheme):
If your book is only available in Hardcover, and the Hardcover price is under $22.00 (U.S.), then the maximum allowable price for your ebook is $9.99.
If your price is $22.01-$24.00, the maximum ebook price is $10.99;
$24.01-$25.00 is $11.99;
$25.01-$27.50 is $12.99;
$27.51-$30.00 is $14.99;
$30.01-$35.00 is $16.99;
$35.01-$40.00 is $19.99.
If your hardcover book is priced above $40.00, you can price your Apple ebook at any price you like.