From the site linked in the article, "Proper Etiquette for Quitting Your Job in Japan":
Show your appreciation to every member of the company, or at least those you have been working with directly. Sweets, small gifts such as mugs, tea sets, a thank-you card or other similar items will be appreciated by everyone. Prepare those for your last day on the job. Usually, Japanese companies will see you off by hosting a small party and presenting you with a flower bouquet, so having something to give in return always makes a good impression. You may also be asked to give a speech, so prepare a few farewell words just in case—but keep it short and sweet.
Skipping these niceties in order to save embarrassment makes the world a little colder.