Since the boards both have ICSP headers and we need programmers anyway, why are we bothering involving the arduino software at all? it adds a lot of complication and has issues with 64 bit architectures. If you simply provided 'hex' files on the web site for the whole firmware for both boards, we can just use avrdude and burn the whole shebang in one go without having to bother with the arduino software or dealing with two different methods of loading firmware (the initial ICSP bootloader, then the serial arduino one).

Generally the ICSP programmer is a extra cost item so it's cheaper for mass end users if there is a tempory bootstrap that permits loading of new programs via a serial port.

The drawback is that it occupies 2K of memory and if you are tight on code space that can be important.

I have blogged on using AVRDUDE with the standard USB to serial cable that we use to burn a boot loader, no reason it couldn't be used to directly load code as you suggest.

Link to my blog [exmrclean.blogspot.com]