Unfortunately they are connected in the eagle file.
It would be possible to disconnect them as the trace joining the two is accessible on the bottom of the board, however you would still be left having to run a wire to bring the NRD pin out.
So really, unless you can set the A5 pin to be an input, and then use the external memory with structs which contain a maximum of 32bytes, and store those structs in the memory aligned at 128byte boundaries, then sadly the external memory capability is not possible.
That right there severely cripples the Due's capability and the number of possible uses for it.