BOE: You are correct to a certain extent about the "rod" being the same. Actually the blank may be the same model. My uncle is a custom rod builder and it is amazing to see the differences in factory blanks alone. You could take a dozen of the same model blank and see that there are subtle differences in them. I am not talking about factory seconds, but production quality blanks. So assuming you get the best of the lot of blanks, a custom rod builder will actually build the rod around the blank and its charecteristics according to your fishing needs.
I am certainly no rod expert, but I do know that the custom rods I have fished with are way out of the league of mass produced rods. IMHO having a "pretty" rod is down on the list of "needs" but if I could afford to replace all of my rods with custom built rods, I would.
Not to take anything away from TH's rods, but you can check
www.featherrods.com and they have some good info on what makes a custom rod truly custom. This includes blank selection, guide selection and placement, reel seats, handles and finishes.