I think I've found more Kitkat varieties at Narita airport's gift shop than anywhere in town.

Sounds like you got on the Haruka.. most rapid trains operate that way and it confused me a bit at first too when the ticket agent for the Mu Sky from Nagoya Centrair asked me if I wanted an all in one ticket or just the express. Then I remembered Japan has a basic fare + express surcharge fare structure. Same with the Keisei skyliner in Tokyo where I needed to tap my IC to get in the turnstile, but needed a Liner ticket to actually get on the train.
Afaik, you can only charge your IC card by credit card if you do it through your phone on the mobile version.

Definitely agree about the soft drinks though, there seems to be like 10 variants of the same brand of coffee in every vending machine. I usually try and stop by a konbini if I'm looking for variety.