No illegal opcodes are used, so it should run on a 65C816. If you're talking about the file system, that'll be FAT12/16/32 and built into the OS. Currently we only have a file system on the ROM disk.
What do you mean modify the OS? The kernel runs in the Shadow RAM and the Atari's OS ROM is turned off. Does Rapidus not run code in RAM under the OS? It's going to be a rather limited in scope if that's the case. It's funny that this is a major concern, and the Rapidus isn't even for sale yet, and I've certainly never been near one. Fortunately GOS will work perfectly well at 1.79MHz. ;)