Given the downside (cost, wait time, warranty, after market) of having a STOCK blank custom wrapped for you, I can't see the point in buying one.
However, I can understand why a fly fisherman would want a trully custom rod made for him/her. A custom rod built from the ground up meaning: you pick the action, stiffness, length, finish, cork quality, grip shape and size, guides, seat fighting butt or not, windings, epoxy coat the blank (heavier) or seal the blank but no epoxy (lighter). The custom rod manufacturer will build a blank for you and go from there. The time is about 3-4 months and the cost is about the same as a premium rod from a major manufacturer because there is no middle man.
The greater majority of "custom" rod manufacturers simply give you custom trimmings on a stock blank. The only truly custom rod manufacturer I am aware of is C.F. Burkheimer in Wasougal Washington - 360 835-1420, Although I am sure there has to be more. I own three of his rods which are the smoothest, non-tiring rods I own. They also enjoy a great resale value for those that know them. The downside to a custom rod is that the buyer has to be experianced enough to explain - in detail - what he/she wants the rod to perform like. However adjustments can be made. For instance, since my casting style has changed during the three years I have owned my Burkheimer 9wt, I now want it a little faster. They will build me a new stiffer Butt section to speed the rod up a bit. I will then have a rod that is almost a mid-flex for clousers and close-up casting and by changing the butt I can go to a faster action. He is going to build me a new sock and tube to house and travel with all four pieces. No way can you have that kind of flexibility and performance with a stock blank.