I don't think there are RN machines and non-RN machines. The credit card machines I've seen in Calgary-area Idine restaurants are all bank-issued. I'm pretty sure Idine is just involved in processing the credit card. Likely, the machine just uses the Idine phone number to process the charge instead of another authorization number.
There is definitely no one selecting who gets miles and who doesn't - the bill can be reflected as discounted, but that seems to be about it. And I've found that most waiters don't even know what RN is or are aware they even offer miles for dining - only upper management does.