Update:
You will not be charged additional Shopify payment fees if you are only using Rakuten Card Reader on Shopify POS. The charges only occur online payments, if you are using Shopify payments and Rakuten together, which is extremely fair. However, you will be charged a monthly payment for the Plan you choose. These are all pluses in my book.
Does Rakuten Card Reader work with Shopify POS? In theory, it should, but still researching. I went ahead and applied for the Rakuten Card Reader and will be testing it myself. This would be great news for the Japanese Community.
In my opinion; When Shopify Hardware and Card readers become available in Japan, I will solely be using Shopify. Hopefully, Shopify will be able to break thru that barrier soon.