This message was posted on behalf of Intel Corporation
As you can see in https://github.com/intel-iot-devkit/mraa/blob/master/docs/edison.md, it is explain the mraa pin distribution. In the case of the Arduino breakout board, mraa uses the Arduino pin distribution. But for the mini breakout board mraa uses its own pin distribution according to the Module's pins. This has not changed from versions 2.1 to 3.0, even though the document itself has been updated a lot, the table hasn't changed. I suggest you to take a look at the link above.
Thank you for the useful link.