I think you mean tftpd64_gui.exe
CloneDeploy is installed in ProgramFiles so program that write to ini files must have Administrator rights (Run as Administrator).
Best run notepad++ as administrator and edit ini files manualy.
It's when using efi mode, in efi each partition and hard drive has a unique identifier, when doing a clone those identifiers are also cloned. When this is checked new values are generated. Generally this is not needed, but if you were to put the same image on two hard drives in the same machine, Windows would not be able to tell them apart with changing the values.
You are free to modify the boot menu as you want. CloneDeploy uses syslinux,ipxe, and grub, you would just follow directions for those bootloaders to modify the menu. In my experience though, most ISO's will not boot over the network because the entire ISO needs to be loaded into memory.