Having a kitchen or cabinetry built for your home versus settling for stock cabinets has many advantages.
First would be the materials being used in the cabinets. Most of the mass producing cabinet companies are looking to save money wherever possible. Using flake board or MDF components in a production line environment is going to save them alot of money over the course of producing thousands of cabinets. In a shop such as ours, building one kitchen at a time, it makes no sense at all. Saving this company $100.00 - 200.00 per kitchen to put out an inferior product just doesn't make sense. We use domestic hardwood and real hardwood plywood to construct every product we build.
The second advantage is the construction itself. Stock cabinets come in limited sizes, usually 3" increments. So if your project calls for a 32" wide cabinet, you will get a 30" wide cabinet with a 2" filler strip. A cabinet builder will build every cabinet the exact size your design calls for. Also a cabinet builder will combine cabinets wherever possible. The idea is a stronger build with the least amount of joints possible. The picture below left is of an above the range cabinet where the microwave or exhaust hood would hang with the two wall cabinets on each side. The difference here is this is all one cabinet.
The picture above right shows a refrigerator cabinet that was built 30" deep to accommodate a 36" deep fridge. We build this cabinet to wrap whatever size refrigerator you have. This unit is also 1 piece. Both of the legs are the cabinet sides. From a stock manufacturer this comes in 3 peices. Again, fewer joints, stronger build. You don't want a kitchen that looks like it went together like a jigsaw puzzle.
The pictures below show the standard scribes that come on all of our cabinets. These scribes are usually 1/4" but can be made larger to accommodate walls that are very crooked or out of plumb. By building the cabinets with these scribes it allows the installer to plane the cabinets into the walls. This eliminates any gaps or the need to add moldings to hide the gaps.