$ check-deps.sh x11-apps/mkfontscale * Checking "x11-apps/mkfontscale-1.1.2" * Missing in RDEPEND and DEPEND: sys-libs/zlib X86_64;libz.so.1 /usr/bin/mkfontscale * Missing in RDEPEND only: app-arch/bzip2 X86_64;libbz2.so.1 /usr/bin/mkfontscale
app-arch/bzip2 is in base/packages so I don't see any need to add a dependency on it. sys-libs/zlib has been removed from there some time in 2011, but the ebuild was not updated back then.
app-arch/bzip2 is not part of toolchain and can be removed from @system set like zlib was, so it is safer to add to RDEPEND explicitly. Also a lot packages already have app-arch/bzip2 in RDEPEND, why not add it to x11 packages? It should not break anything.
Done.