For what it's worth, my April 64 coupe (a 68k mile car that I've had since 1979) has the P/S box with manual steering. The car also had the bracket installed for the hydraulics on the left frame rail, with no witness marks that would indicate that anything was attached to it. It also has assembly line style manual tie rods, and no evidence of the power steering pump ever being there.
My theory is that the worker that installed the box and bracket were one and the same, since they are in close proximity. Production being fast and furious in those early days, it was probably an easy mistake to make. Ford never saw fit to change it or remove the bracket, if they even noticed.
That being said, the manual and power box seems like they can be interchanged.