Freaduino Leonardo is an Arduino Leonardo 100% compatible board. It is based on Arduino Leonardo design. So you can use Freaduino Leonardo as Arduino Leonardo. All code, shield and IDE for Arduino Leonardo are also valid on Freaduino Leonardo.
Some visible improvement on hardware make Freaduino more flexible and easier to use. For example: 3.3v or 5v IO selectable allow you connect some 3.3v modules (such as XBee) to Freaduino directly. Using miniUSB interface, SPI bus breakout make bus connect easier.