S&W guys tend to be fixated on version codes. They explain what modifications have been made from the origional. In some cases, it's to fix a design issue. In others, it just denotes a slight change, such as a thinner or thicker front sight, etc.
In the case of the 686, some early models were akin to 1970's automobiles. The plant made them, and the local mechanics fixed them. Some of the origional Bangor Punta Corp guns had issues with barrel to cylinder misalignment, uneven forcing cones, hammer bushings failing, and an issue with the hand.
The Custom Shop guns are nice and worth the money if the mods are what you need. If you will be changing anything, you might as well buy a cheaper older model and build what you want.