The transit without visa is 144 hours now in Shanghai it will require a ticket to another country than Japan. It is not visa free entry, it is a visa free transit, so you will have to come to China from country A and continue to country B. You can return to Japan after another country, but not direct.
If there is not an itinerary in place that satisfies the full route of the ticket there may very well be a denied boarding at the outset. Arguing that your friend will get the visa in Tokyo is not necessarily a helping point as the Chinese embassy in Tokyo does not issue tourist visas.