If you're already using another tool to generate the .hex file, why upload it with Arduino?
Lets say you start with an arduino and move on to AVR studio now because you move on to a new ide wouldn't mean that you need to buy new hardware.. I think the FTDI bitbang can be used to program most Atmega ICs and perhaps including this as a standard feature can add the face of a programmer to arduino after one has had enough playing around with the arduino. Simple - 1 piece of harware that can do more at the same price...