The difference is in the frame. The S-Works bikes use a different carbon lay-up. The S-Works frames are lighter and stiffer. Also they come with ceramicspeed BB as standard. I believe that they are built in a different factory and with a higher level of quality control.
The off the peg bikes do have all top of the line components, but you can buy the frame and put on it whatever you like. Whether it’s worth the extra money is purely subjective.