flight Tokyo-Shanghai-Soul-Tokyo qualifies for visa free transit?

Yes that is ok.

TYO-SHA-SEL-TYO is clearly a vaild itinerary as far as Chinese immigration is concerned, and I've done similar routes many times. The only possible problem could arise when you check-in at Tokyo. If the agent wants to see the Chinese free transit rules on Timatic they have to put S Korea as the destination and China as the transit.