Uhm. this has a sense for me. Since today, I've only tested the 1284P on a breadboard because I didn't want to make a board for the serial programming using the bootloader if I wasn't SURE that I could do that to upload a sketch.
Well that leaves you in a catch 22 situation doesn't it? 
So maybe make provisions in your PCB to install a resistor/cap filter near the RX0 pin and just don't install the components and jumper around them with a wire jumper or a 'zero' ohm resistor if testing proves they are not required with whatever layout you end up using.
Lefty