The kind folks at ePayments.jp went out of their way to conduct extensive field tests and contacted me that my post reported incorrect information, I am thankful they did so. I should have done a better research job before posting and apologize both for the error and any confusion resulting from it.
When Apple introduced Apple Pay Japan in October 2016, the official release stated:
When paying for goods and services on the go within apps or Safari, Apple Pay works with iPhone 6 and later, iPad Pro, iPad Air 2, and iPad mini 3 and later. You can also use Apple Pay in Safari on any Mac introduced in or after 2012 running macOS Sierra, and confirm the payment with iPhone 6 or later or Apple Watch.
This has not changed for older Japanese iPhones in iOS 11:
However some Japanese iPhone 6 and 6S users were confused when adding Apple Pay cards for the first time in iOS 11. Apple Pay Japan cards in Wallet display the iD or QUICPay store payment logo artwork regardless of the device, because of this and rumors that Japanese credit card companies are considering NFC Pay support, some people thought iPhone 6 and 6S running iOS 11 could be used with NFC Pay (EMV) store terminals. As Apple documentation and field tests make clear, they cannot.
In theory Apple could add NFC Pay support in iPhone 6 and 6S for Apple Pay Japan Region set credit cards that can use it. But just like FeliCa support for non-Japanese iPhone 7 models, Apple is not going to re-qualify and re-certify older devices.
Users who want global FeliCa, NFC switching and all the other goodies of iOS 11 Apple Pay need to upgrade to iPhone 8, iPhone X or Apple Watch 3.
With the NFC switching capabilities of iOS 11 Apple Pay, Apple quietly activated Apple Pay Japan for older non-FeliCa NFC capable iPhones such as iPhone 6S. Surprised users with Japan issue cards that support JCB J/Speedy and Mastercard Contactless can add them to Apple Pay and use them at stores with EMV NFC-Pay ready readers. Japan issue American Express cards should be good too but I have not confirmed them in the field yet.