Okay, apparently I can just create my own "hardware" hierarchy inside ~/sketchbook/ and modify files like CDC.cpp as I please from within there.

So I've done that, and simply hacked CDC.cpp to use 520 byte serial buffers instead of 64 byte buffers. This cuts my firmware download time by half. It now takes 8 minutes 53 seconds to transfer the 2MB image to the Arduino. Much better!