You can, but let me make a similar suggestion. I now hardly touch my Arduinos because what I do is put an ATMega328 on a breadboard or solder them up with an ISP 6 pin header like that and write my code in the Arduino editor but write it to the board using an Atmel Dragon with the programmer in Atmel Studio. There is no bootloader under these circustances either and you can use 328 chips which are $1.81 each in quantites of 25 from Digikey. Since that device will look like a STK500 to Atmel Studio, you can send it up the same way.
From the current project: