I can confirm this can be done. I had all sorts of trouble with compiling bootloaders and ended up using the precompiled sensebender micro bootloader (which uses pin 8 for CS (SS) activation of SPI memory). The way around this for now was moving the rs485 to the hardware serial port and disabling all debug output. I went with a 3.3 Arduino Pro Mini and level shifter for the MAX485 module (thats all i have here). I've done 3 firmware updates over the wire using MYSController and so far am impressed with the results. I would like to compile a new DualOptiboot and move the SS pin but can't seem to make this happen.
Very messy breadboard, but just for an idea.