As far as I can tell, they work exactly the same way. I was able to use my iPhone 6 at an NFC terminal (built for MasterCard PayPass/VISA PayWave) at Dublin Airport where nobody had ever used it before in that fashion.
I have a feeling the MCX participants and card issuers are going to come to an impasse over their respective agreements. All the issuers have to do is require that terminals capable of NFC (for the purpose of accepting PayPass/PayWave) not have the functionality disabled. This will put the merchants in a bind and force them either to replace the terminals altogether, or re-enable NFC.