You're right, when using the SMC you need both PC26 and PA29 as they both have functions with the SMC.
As they are shorted together you are screwed.
set PC26 as an input when you are using the SMC.
Doesn't help I think, you'll lose A5 if you do that.
No I think the Due cannot use external memory, if so that's a major shortcoming IMO.
The connection of those two pins make no sense as far as I can see, it's just possible that the PCB doesn't actually do that and the schematic is wrong. I think Massimo said the other day that the MACB connector is not on the PCB, not just DNP but not even allowed for, and yet it's on the schematic. So one has to wonder about the accuracy of the schematic.
It's 2AM here but tomorrow I may grab the Eagle files and have a look at PC26 and PA29.
Rob