Could you change the bootloader to look for some kind of header or footer byte sequence in the hex file (that could be appended or pre-pended to the file in the build process)? Unless I misunderstand where this delay occurs...
No, the delay is well before that. It's to see if there is any valid activity on the serial receive line at all right after a power-up or reset. If there is and it's a proper signal, then the bootloader stays active servicing valid commands from AVRDUDE via the IDE connection. If there is no serial data activity after the delay period times out, then the bootloader jumps to the existing sketch already resident in memory.
I've noticed that lots of development boards use a simple switch or removable jumper to activate the bootloader or not on power-up or reset. While it does take up a digital input pin, it does eliminate a delay on programs starting.
Lefty