Nothing really. You probably already understand that a well adjust sora is better than a badly adjusted Dura Ace. All Shimano bikes are made to be adjusted very easily, and even the simple man can adjust their derailleurs to perfect shifting. Unfortunately many bikes shops don't have the time to adjust everything to perfection, because then to build the whole bike would take double the time. Then when the bike is sold, most owners never even touch the configurations, and thus the people with problems think that sora sucks.
The story continues. They upgrade to Ultegra or 105, and the bike shop probably takes a tiny bit more time to assemble the bike, and theres a bigger chance that the gears will work perfectly.

Just for your information, this is the nob you can turn to tune your rear derrailleur, usually works a treat.