The Optiboot bootloader allows you to easily compile for any serial port without any modifications to the code. There is a fork of the Optiboot bootloader that supports ATmega2560. So if you really want to compile a bootloader to use a different serial port on ATmega2560 for upload it can very easily be done. That is exactly what has already been done for you in MegaCore.
Compiling the stock Mega bootloader will definitely be more challenging, but why bother when optiboot is so much better?