The manufacturers have gotten quite clever. There are many examples of what you are suggesting. Specialized Body Geometry is just one. You buy the road shoe and it comes with a neutral (completely flat) foot bed insert. You can then buy a low, medium or high arch support insert to swap. Or go one step further at selected Specialized dealers and get a custom thermo-molded insert. All the other major brands have similar options. Or just buy a third party insert from a shoe store or athletic store and experiment. Many, many options.

As far as overall comfort; good socks, practice fitting the correct shoe and setting up the cinch just right has made shoe comfort issues a thing of the past for me. Reference -- I'm using Specialized Torch 2.0 and a Body Geometry Red insert.