It’s an advanced level programming header that could be placed OVER the AVR microcontroller to save space and to make fast and easy/plug ‘n play connections. The first prototype was developed for the Attiny2313 and did just that; it connected the programming header pins to the appropriate pins. This is the basic straddling header with a 6 pin header. The ‘definite’ straddling header was also developed, that also included some stuff that almost every AVR circuit needed and that was more or less ‘fool-proof’.
The definite header has decoupling capacitors of the required value so as to save the controller from large switching current. It also provides ease of accessibility to place a crystal of the highest frequency the specific AVR can handle on the board, including the SMT capacitors. For the ‘breadboard’ pins they have provided extra-long pin headers. These can be fed ‘through’ the board for included stability. There is also an extra pin next to the reset pin is on pin D0, so you it to add a Led there to make it easy to flash your first blink-led program to test your AVR programming chain (and/or the specific AVR). The only downside there is, that if you are going to use the serial on higher speeds, the Led could be bothersome.