You may want to download Clover Configurator for Sierra, then mount the EFI partition with EFI Mounter v3, double click config.plist, select "Install Drivers" in the left pane, notice the boot device - change it from "Null" to "Sierra," exit - which should write out back to the EFI partition.
Notice that when you start EFI Mounter v3 that it will show a disk and the scroll bar doesn't work. Highlight it then use the down arrow to get to the EFI partition/device that you want to mount.
In case anyone is still struggling with this: If you've got Windows installed you can use EasyUEFI to add a boot entry for Clover. Click manage EFI Boot Options, then Create a new entry, select the EFI partition, then EFI\CLOVER\CLOVERX64.efi
If not, you could try adding them manually in the UEFI shell in Clover, using something along the lines of "bcfg boot add 0 fs0:\EFI\CLOVER\CLOVERX64.efi Clover". (I might have gotten the syntax slightly wrong.)
I think the problem is more with Clover than Unibeast. I had the same problem after installing Sierra. Clover did not have a boot options menu for the HDD after installing Clover to my HDD. I simply booted using a USB drive that contains an older version of Clover (my previous El Capitan USB installation) and it then gave a boot options menu for the HDD. After using the older version of Clover to add the EFI boot entry I could boot from my HDD's latest Clover version.