The 2560 bootloader fixes haven't made it into production Arduino MEGAs yet, so it will still have the "!!!" bug.
There is fixed SOURCE here: https://github.com/msproul/Arduino-stk500v2-bootloader
(but no new .hex file.)
The other issue to be aware of is that a lot of programmers have troubles programming beyond the 64kwork limit (including ArduinoISP and Adafruit's USBTinyISP), so even if you compile the fixed source to a .hex file, you may have trouble getting it loaded onto the chip.