I does not matter. I program in Python on the Arduino Breakout and it works really well. You need to install the mraa library. The good thing about the Arduino Breakout is that your I/O are already level shifted to 5V so it's easier to connect to the external world. You also have an ADC on board.
as speccy88 said: both boards are supported by mraa (see intel-iot-devkit/mraa · GitHub). And both Python as well as Node.JS can make use of mraa. Probably not every feature is supported likewise in both of them. For Node.JS you can use Intel® XDK IoT Edition | Intel® Developer Zone which gives you an IDE at hands. For Python there is currently no IDE support available I am aware of