Can you even get one CD to boot on both ix86 and ARM or PowerPC? Even if you can, along with getting the right kernel to boot up, you should be to symlink in the correct binary directories for the architecture.
I'm having a lot of trouble finding any case where FatELF can't be replaced by shell scripts and symlinks. You want to support both ix86 and AMD-64 with your game; have the executable name run a shell script that runs the right binaries.