@m3x
It appears that Sam460 runs the AMCC460 slightly (15%) overclocked. Is this similar to the overclocked 440 models where the memory bus is slightly underclocked? Does this explain why 7447 166MHz DDR-333 memory interface appears to be faster than Sam460 DDR2-400 memory interface?
You have some information slight wrong and outdated

On the Sam440ep models, the DDR runs at the nominal speed (133 Mhz) on the 667 Mhz and 800 models, and run overclocked on the 733 Mhz model (147 Mhz)
There is a pci-update which overclock the PCI unit on the SoC, but due constraints in the internal multipliers, is not possibile to overclock both DDR and PCI unit, and thus on this model the user may choose to keep the original setup or to overclock the PCI unit.
On the Sam460ex the DDR is overclocked as the CPU. The reason why right now the reported speed is somewhat low is due the very conservative setup done by U-Boot, and because APM is still updating their autoconfig code.
I was able to enhance the speed just recently and now the figures are as follow:
Read: 350 MB/s - Write: 560 MB/s
Next U-Boot versions for our board will include modifications on the DDR config code to achive higher speed transfers.