[preview]

The FPGA fabric will also have to be configured whenever power is lost. This probably includes the low power states of the Atom since the FPGA wasn't designed to support it. It would make sense for this to be part of the BIOS-level code since the FPGA is useless until configured.

There is a savings in board space, but, otherwise, this solution provides no additional value. You can already connect an Atom processor and FPGA through PCI Express.

[iwr]

The configuration would be saved in Flash memory and loaded at boot time. Also, you'd need to reboot the FPGA each time a new configuration would be written in.

I am not yet aware of FPGA-like chip architecture that can be reconfigured dynamically.