genkernel as default don't include "xhci-hcd" module into initramfs image, this prevents to boot from external USB3 disk.
This has been committed to genkernel HEAD: http://git.overlays.gentoo.org/gitweb/?p=proj/genkernel.git;a=commit;h=1e92078650d3f7c27beaf97dc55b1aabf3acfb79 It will be in genkernel 3.4.40.