There are lots of semi-custom cabinet lines that offer more than a stock/builder grade cabinet. What cabinet lines are you quoting? Two of the semi-custom lines that I carry will also custom build specialty cabinets per my drawings. Showplace and Shiloh. KraftMaid offers a papertowel unit, I believe, but not built in to a cabinet. But...You can also use parts to build a papertowel holder (ie. brackets and a rod). If you want a papertowel holder built in to a base cabinet, you could do a custom microwave cabinet with a finished interior and custom sized top opening. Good luck.

Your terminology "giving up on the custom line" confuses me a little. When the term "line" is used I think of factory built cabinetry (ie mass production). Custom to me is represented by a local cabinet shop that is producing a one off product specifically built for the sizes of your kitchen, Some "lines" of cabinets are semi-custom where the manufacturer can build just about anything. This, however, can cause some cabinet lines cost to increase significantly. If you haven't already, you may want to ask your builder to seek out a local cabinet maker for a price. Good luck.

Fifteen thousand does sound a little steep for a built-in paper towel holder!