I do, fortunately, not know about the Atmel chips, but what I have read so far seems to indicate that this NXP info may apply. I have done this very thing with SILabs chips.

Could I create my own 'C' bootloader that has a custom 485 interface built in
Yes, but I would use assembler
(which would allow me to use addressing to specify processors) and use a custom protocol to have a controller send the hex data, a bit at a time.
I would use the source from Atmel as a base and just add the 485 stuff while keeping the actual record format and store functions as is. If you go too far in 'personalizing' the bootloader you will end up having to make a ton of PC code, if you 'go easy' on the 'personalization, you may end up being able to use FLIP as is.

Could my bootloader then receive these packets, and store each one (after CRC checks) into the code flash memory until they are all received and then boot itself back into normal running?
see above

I already have a 485 interface and protocol that is used during normal running of things. This allows the controller to speak to each of the 9 processors individually (by address) and use broadcasts. Could I just strip out this interface and use this as a foundation of the bootloader?
Yes

Is the bootloader, in essence, 'just another app' but limited to 2k, and triggered to run conditionally?
not just 'limited' to 2k but running in its very own 2k of code memory which is not part of the application code memory.

Erik.