Kiwi has it right, throttle bodies and cams are different, and the map that's loaded in the ECU. Everything else is the same, so upgrading to the same HP won't be difficult once somebody figures out how to crack the ECU. A German company has done it but I haven't been able to reach them. I also think that you will be able to get most of the power with an aftermarket fuel controller, probably even more than a stock F800GS because those run pretty lean. Ignition timing won't make as much of a difference.
I've got both F800GS and F650GS throttle bodies here, will have to see what the difference really is when I find some time in the shop.