The main difference is that the single file doesn't Factory Reset the phone after flashing, but the 4 file firmware does factory reset and remove absolutely everything and make it like an out of the box phone.
The 4 files are called Binary Firmware which contains all the files in certain order:
BL ,Bootloader contains all the boot files
AP Contains all the system and recovery files.
Modem/CP contains phone network and wifi software.
CSC Contains PIT file and Cache removing IMG which puts all the files in order and repairs any damage firmware has before.