after a clean install, mount outputs (amongst other things) tmpfs on /mnt/.init.d type tmpfs (rw,mode=0644,size=1024k) removal of the directory /mnt/.init.d does not solve the problem
I fail to see how this is a problem? Gentoo uses /mnt/.init.d as a small (1MB) ramdisk for dependency caching of /etc/init.d services.