In this case I am "avrdude" savvy and have tried the code that you have provided:
avrdude -p at90usb82 -F -P usb -c avrispmkii -U flash:w:MEGA-dfu_and_usbserial_combined.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
with changes to fit my development environment...
And some of the additional derivatives on this theme have included:
avrdude -C avrdude.conf -p m16u2 -F -c avrispmkii -P COM8 -U flash:w:\arduino1\hardware\tools\avr\bin\Arduino-usbserial-atmega16u2-Mega2560-Rev3.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m
In the previous case I have tried a variety of Arduino hex builds as provided on their sourceforge site.
As stated I have an AVR One as well and although it can not program to the 16u2 in JTAG mode, when I add the ISP connector it does not work either.
I have also tried to use the programmer provided within Studio 5 and Studio 6 and although as stated I am able to program via the ISP to the 2560, the 16u2 remains a mystery, even with the hardware reset as indicated for the 8u2.
There seems to be quite a few users having a great deal of difficulty with the 2560 or rather Arduino's delivery and lack of support for the chip and its 16u2 R3 add-on. I don't understand the total lack of support either by Arduino or Atmel. I do understand the nature of open source but these boards are being sold in retail outlets and if plugging them in and simply trying to load a simple blink program onto them via the IDE causes this amount of difficulty then perhaps some thing need to be re-examined. Either by Arduino or the consumer (you and me).
As you can see, there is some frustration here and I can sense it in the OP follow-on posts as well as other threads regarding the same issue. However, I am not willing to throw in the towel just yet. After spending as much time as I have in trying to figure this thing out I believe a certain form of stubbornness has settled in, on my part and giving up isn't an option. So, like so many of you I shall sally forth and keep at it.