> I guess most people will buy a SATA controller card and put in that slot to be
> able to use at least 2 units

From the Sam460ex user manual:

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The current U-Boot version support booting from the following devices:
- SATA2 hard disk connected on the onboard controller port J15 (* check notes)
- SATA hard disk and/or DVD connected to a Silicon Image 3112 controller on PCI slot
- SATA hard disk and/or DVD connected to a Silicon Image 3114 controller on PCI slot
[...]
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Booting from SATA card in PCI-e slot seems not possible.