For ease I will use “Japanese TMB” to refer to World Challenge Best of Japan, Juniors division (exclusive to Japanese players who won regional competitions and awarded the holo personalized trophies) and “International TMB” to refer to the event Jason attended for players around the world, no official tournaments needed to be invited depending on which area) in this post.
The 2000 World Challenge Best of Japan was split into two tournaments, one for the Juniors division and one for the Seniors division.
The Juniors division 2000 World Challenge Best of Japan, aka the Japanese TMB, took place on August 26 in Hawaii to coincide with the International TMB. Toshiya Tanabe was the 1st Place Winner for the Juniors Division in Hokkaido, which won him entrance both to the Japanese TMB and the International TMB. While stressful for any competitors to go back-to-back, it’s easier than to plan two separate events both in Hawaii both in August. If you read Jason’s post closely, you’ll see that he basically spent August 26 doing fun casual activities, and August 27 actually competing. Meanwhile, the Japanese players were having their Japanese TMB on August 26. Because of the language barrier, Jason may not have realized the kid he was facing had already been through a major tournament the day before.
The Seniors division 2000 World Challenge was a separate event that took place in Japan and is likely the source of your confusion. Remember that in 1999, the Juniors division won the “Tropical Mega Battle No. 1/2/3” cards and the Seniors division won the “Super Secret Battle No. 1/2/3” cards. So the TMB theme was already there for Juniors prior to the International TMB.
Another reason for your confusion is unfortunately Bulbapedia has some inaccurate info. I assume you are writing “The other was a tournament in Japan for children who either didn’t make the top placement for the international event, or weren’t able to attend.” due to Bulbapedia’s comment you quoted:
“Overall winners of the Tropical Mega Battle regional events would represent their country in the World Exchange Battle in Hawaii while the remaining top ranking players would compete in a domestic “Best in Japan” final. Both of these events were also held in late August 2000. The champions of the Secret Super Battle and Tropical Mega Battle “Best in Japan” finals were awarded Holofoil No.1 Trainer cards bearing their photograph superimposed on the illustration.”
Based on this you would assume the International TMB was the main competition and the Japanese TMB was some small less-important event for people who didn’t make the cut. I am not sure where they got this from. The “Best in Japan” final was by far the more prestigious tournament in Japan. All the primary sources from this period emphasis it over the International TMB. Each of the 8 First Place Regional winners were invited to the 1999 TMB and it was likely the same with 2000. Other Japanese players also were invited but they did not get to compete in the Best of Japan, only the Top 8 regional winers did. You had to be the best in your region just to be invited. Also not to insult the International TMB, but it was a more casual event, where you were given specific cards to make your decks from and limited to only 90 to choose from, and all the prizes were participation based, not personalized holo numbered trainers. It is likely the Top 8 Regional winners cared much more about winning the Japanese TMB than the International TMB.
Some helpful photos:
**Information that trophy cards were awarded to the Japanese TMB winners in Hawaii alongside the International TMB:
Zoom to see photo of Jason and Toshiya Tanabe (also confirms he is from Hokkaido)
Results of 2000 World Challenge, Hokkaido Regional Tournament - Toshiya Tanabe 1st Place Junior:
Here is information about the Japanese TMB and the Seniors Division tournament (SSB); you can see Toshiya Tanabe in the same Puma shirt as on his trophy card, proving that he won 3rd Place in the Japanese TMB on August 26:
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Edit: I was browsing pokemon-card.com for information on the upcoming Japan National Championships and saw that while the 1999 Japanese TMB was indeed held in Hawaii, the 2000 one was held in Tokyo. It looks like you saw this as well based on the articles on the site! So unfortunately, my research was completely in vain and inaccurate in regards to 2000, though hopefully helpful for your 1999 article.
www.pokemon-card.com/20th/chronicle/