As per bug #401899, x11-drivers/ati-drivers should use virtual/modutils instead of sys-apps/module-init-tools. Reproducible: Always
It doesn't "use" it at all, in any way. It's not an RDEPEND or anything, and it shouldn't be either.
True, there is no trace in the ebuild, but equery claims it has the depency. $ equery d module-init-tools * These packages depend on module-init-tools: app-emulation/virtualbox-modules-4.1.8 (kernel_linux ? sys-apps/module-init-tools) sys-apps/rescan-scsi-bus-1.29 (sys-apps/module-init-tools) virtual/modutils-0 (sys-apps/module-init-tools) x11-drivers/ati-drivers-11.12 (kernel_linux ? sys-apps/module-init-tools)
That one comes from linux-mod.eclass and this issue has already been spotted in bug #401899
OK, now I also found the correct report bug #404193 Sorry for the havoc then.