Ok, I just wanted to post my progress.
I was able to compile and upload the terminal code posted on the original thread to a Due board using IDE 1.5.2 using the programming port.
The original ADK2012 IDE required the native port.
After digging for a few days and comparing with the Google released ADK2012, I realized the problem is with the arduino reset code built-in on the libs to erase the flash when native port is used for programming (AKA open serial at 1200bps).
By having this code enabled all the time will disable the native port from ever being able to act as OTG port.
But the trick is that if this code is not enabled, you won't be able to erase flash and upload using native port on a single shot. You will need to press the ERASE button.
In my case, I'm never planning on using the native port for uploading code anyway, so my solution works out great for me.
My solution was to create a new board reference in the boards.txt file and remove the flags for the CDC serial on native port.
New_Board.name=My Own Board
New_Board.upload.tool=bossac
New_Board.upload.protocol=sam-ba
New_Board.upload.maximum_size=524288
New_Board.upload.use_1200bps_touch=true
New_Board.upload.wait_for_upload_port=false
New_Board.upload.native_usb=false
New_Board.build.mcu=cortex-m3
New_Board.build.f_cpu=84000000L
New_Board.build.core=arduino
New_Board.build.extra_flags=-D__SAM3X8E__ -mthumb
New_Board.build.ldscript=linker_scripts/gcc/flash.ld
New_Board.build.variant=arduino_due_x
New_Board.build.variant_system_lib=libsam_sam3x8e_gcc_rel.a
And add an ifdef on the USBCore.cpp to disable the CDC code.
#ifdef USBCON
Original USBCore.cpp code goes inside the ifdef. I can't add or the post is too long and exceeds the maximum allowed length of forum, which is 9500 characters.
#endif // USBCON