Is it all a matter of where you send the data? I mean to say, if they're both a form of Serial, what's to stop you connecting a Serial cable correctly through the ICSP and burning the bootloader?
The ICSP uses a different protocol then the serial data link from the Arduino IDE. The ICSP requires discrete control signals, data in, data out, clock and reset. The data is clocked into the AVR chip one bit at a time and does not involve 8 bit data characters like the serial converter that uses the bootloader to program the chip via the Arduiono IDE.
Different methods to accomplish the same task. AVRDUDE is the programming software that accomplishes the task of loading your program, but the Arduino IDE only launches AVRDUDE, telling it to use the Arduino bootloader serial data method.
Lefty