As an example, the Clonezilla Live USB Documentation supports both manual installation from a .ZIP archive, as well as automated from a .ISO file. Overall, both processes are the same: if you can boot the system from the USB key, you're done and it works - and indeed, both methods will yield this result.
You can use a utility like you mentioned (Unetbootin, Universal USB installer, Tuxboot, etc...) to create a bootable USB key via an ISO file, or you can manually do what the program does. This is deemed the "manual" method, and entails downloading the official .ZIP archive, manually formatting your USB key if required, extract all the files to the key, and executing the included script to make the drive bootable.
Two types of files are available, iso and zip. The former one is for CD, the latter is for USB flash drive