This template is a base for creating Arduino projects on the ATmega328 without using the Arduino IDE. Personally, I prefer to use the Arduino Eclipse IDE (http://eclipse.baeyens.it/) for ATmega328 development. The biggest advantage for me is the pin mapping in atmega_pins.h. In my development, I generally will develop without the actual Arduino board. As the mapping on the ATmega328 is different than the Arduino mapping it simplifies my workflow.
If you want an example of ATmega328 development without the Arduino board, take a look at this reference. https://www.arduino.cc/en/Main/Standalone