1. If your installation of 10.11.4 did not create a virtual disk for the physical OS (El Capitan) disk, the command may not be relevant.
2. If your EFI partition (Clover boot location) is on the same physical disk as El Capitan partition, Clover installer will only identify the "DISK" and cleverly installs the updates into EFI partition. BTW, r3320 also worked the same way for me.
3. In my case, when the virtual disk existed, Clover installer can only see the virtual disk (and I have only one physical disk), therefore created an EFI holder on El Capitan partition.
Cheers