makepasswd - this is a very old program(1998 year in the man page) and not supported by anyone other than Debian. We can assume the current version of Debian is the upstream.
The option "--crypt-md5" is known in other linux-distros for a long time. Strange that it does not exist in Gentoo. Patch from Debian is adding support for this option.
Patch from http://packages.debian.org/stable/admin/makepasswd (makepasswd_1.10-5.diff.gz) added to makepasswd ebuild.
I agree with the crypt output feature, but disagree with the switch from /dev/random to /dev/urandom