I created a Rakuten Kobo bookstore account outside of Japan without VPN and I’m able to link it to my international Kobo.com account after I changed my international Kobo.com account settings to Japan.
My Amex card didn’t work but the Mastercard works. So I continued using Mastercard.
The ebook you bought should appear in your My Books section in your Kobo app or Kobo ereader once you have linked the Rakuten Kobo and international Kobo accounts together. You can try buying a free book (not just free book samples) to try first.