The difference is that you will set up a Square Enix account depending on your region - so NA for USA, EU for all PAL regions, and JP for...well, Japan. This also counts for your payment. You must, therefore, register and play using an account under the European Square Enix site if you are part of the areas which it comes under.
Log-in, servers, and updates are universal around the world.
A security token is recommended but not needed to log in. It provides security in case someone hacks your password, since they'll then need your token code to log-in to your account or to play.