The site doesn't describe any real problems.
In a simple way: please look at coreutils-8.20.ebuild that has to move a lot of binaries from /usr/bin to /bin:Also I don't see how the current dir tree is not compatible
with gnu autoconf/automake.
So, how would this work for me who have /usr on a separate harddrive?
And what would be the benefit? To me, mentioning Fedora, makes the alarmbells go off...