If you name the transit authority doing this, it'd be possible to look at what the iPhone/Android phone is actually doing. One possibility is the information being shared when using the NFC isn't your CPAN or DPAN at all, but is a 3rd identifier with which they deanonymize you.
If you use an EMV card in transit, then the Visa/MC rules say that the same card must be used to pay for the fare.
Transit providers are not allowed to use the EMV card purely as "identification".
I answered elsewhere on the thread about how the transit provider is able to use the EMV as an identifier after it has been used for payment, with a one way hash sent to the transit provider.
