Finding arduino bootloader version?
In all practicality; put a known boot loader on it. Because if it is a problem version you will need to replace it anyways.

The Mega uses STK500 protocol. Which only shows a command to read its type (or signature) and not its version of firmware.

It is a good exercise, but not really worth the time to go deeper into it, as programmers are cheap and or you can use another Arduino as the programmer.