Prefix support is half-done. All ROOT references need to be replaced by EROOT references for the module to work correctly under Prefix. I've patched the ebuild to fix this in the meantime.
Fixed in git, I'll wait a bit for more changes needed due to recent developments in ruby.
+*eselect-ruby-20120106 (06 Jan 2012) + + 06 Jan 2012; Alex Legler <a3li@gentoo.org> +eselect-ruby-20120106.ebuild: + Additional prefix support, bug 396701 +