If you can't disable LTO in gcc >= 4.6 (in toolchains.eclass), then there shouldn't be any ewarn related to LTO in pkg_setup ebuilds >= 4.6.0. Reproducible: Always
the point of the warning isn't that lto is available, it's that you tried to use it. i.e. using gcc with lto support available is fine, but don't be surprised if use of -flto eats your system.