I dunno. If I can get a development board or something for this, I want to start playing around with FPGA development, but I'd need a lot more practice before I'd commit to something like that. But haven't projects like Minimig already implemented much of the Amiga functionality on FPGA? Could that groundwork be borrowed for use with this?
Pretty much *all* of the Amiga functionality. With Natami and FPGA Arcade it's even closer and at least in the case of Natami clearly surpassing the original hardware (faster, new features).
The Minimig cores are freely available, so an Atom with FPGA on board could - assuming the FPGA is big enough - possibly be used with it. The question would be what the purpose would be. You don't need the Atom if the purpose is "just" to re-implement a classic Amiga - you can still buy 68k CPU's and/or you can use one of the available M68k cores (or in the case of Natami they're developing their own - so far proprietary - improved M68k "successor" core that's intended to be backwards compatible).
But for something like an AROS system with chipset compatibility with classics it could be interesting. E.g. run AmigaOS or M68k AROS on the FPGA, and use Janus-UAE or Emumiga type methods to "bridge" windows etc. to the AROS host system. The thing is, though, for things like that the system would overall probably be faster if you'd just use a faster x86 and emulate the chipset since the Atom's are horribly slow.
A "Minimig + faked bridgeboard" could be fun - using the Atom as a co-processor to run x86 apps and/or to speed up certain things similar to how PPC cards were/are used on classics and/or how the bridge boards for the A2000's worked.