I too am wondering about how the FPGA will be accessed from software. I can only assume that there's a built-in DMA interface, and that only one process can grab the FPGA at a time.
http://www.fpga4fun.com/ is a nice site with stuff that novices can have a go at creating.
There's also a sister site (http://www.knjn.com/) where you get hold of inexpensive FPGAs for tinkering with.
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.
I am not yet aware of FPGA-like chip architecture that can be reconfigured dynamically.