I'm nor so sure you can get AVRDUDE to burn two separate hex files (as in sketch code and bootloader code) as I think it has to erase flash before it burns the flash. At least I know the behavior of first burning a bootloader via the IDE and then uploading a sketch with the IDE upload using programmer, results in the sketch being installed but the bootloader being erased. Perhaps using AVRDUDE in command line mode one can work around that but I don't recall ever seeing that process documented around here?
Lefty