but I am trying to interact with a system that starts talking on the bus ~750ms after power on, and naturally the bootloader delay gets in the way
There is a bootloader available written by "Lady Ada", Limor Fried, of Adafruit Industries. It has virtually zero time delay on power up. I have used it and it works well for must start quickly applications:
http://www.wulfden.org/TheShoppe/freeduino/ADABOOT.shtml
Lefty