Oddly enough, you can't link against a shell script...
Multi-arch binaries are not tremendously useful. Multi-arch libraries are very useful. Yes, directories once again could be used, but various "standards" groups have already agreed on a defacto lib vs lib64 multi-arch setup which totally falls apart in the face of anything besides a single pair 32-bit and 64-bit architectures. I'd much rather have just seen the platform encoded in the library sonames and filenames (.e.g libfoo.so.linux.x86_126.96.36.199 vs libfoo.so.bsd.ppc188.8.131.52), but alas it wasn't up to me to make the call.
Oddly enough, though, multi-arch executables are actually a better solution than directories, because the question comes down to which directory to search for executables. We could have /bin broken into /bin/i386, /bin/i586, /bin/x86_64, /bin/ppc, etc. with the PATH environment variable used to select which to search... but it'd be ugly and force changes on every installer, package set, and so on. Granted, I don't find multi-arch binaries particularly useful, so I have no problem with packages or installers just figuring out which binary to install.
However, people who use NFS-mounted root directories across a variety of systems could get a big boost out of something like fatELF. A single root directory tree could theoretical serve thin things running both native i386, native x86_64, or native ppc code. Less maintenance and all that jazz.
All at the cost of a little extra disk space on a server and a little bigger packages to download on the 50mpbs pipes you can get for cheap these days.
That said, for the purpose fatELF is obstensibly being designed for (commercial games), fatELF is just silly. The installer can just install the proper binaries based on the target architecture. An installer shell script can pick which installer binary to run (or better yet, the Linux software distribution scene could get its head out of its ass and supply a standard distro-neutral installer framework that's installed in the base package set for every distro like how it should've been done 15 years ago).