As Clover is only 1MB, I have added the 64--bit Clover version to the MPI Tool Pack. This means that all image .imgPTN files made using MakePartImage will include Clover. The Clover menu option will only appear in the menu if a \EFI\BOOT\bootx64.efi file is present and partition 1 is on a FAT32 partition.
If you have converted a linux ISO to a .imgPTN file and it has a bootx64.efi file, the Clover menu item will be displayed.
if you don't want Clover to be added to your image's menu, the simplest option is to rename the CLOVER folder to something else and it will not be added to the image - alternativley, after you have made the image, just delete the \EFI\CLOVER folder from the image (or rename or delete the \boot7 file).