During development, it is a very common task to combine the 4 elements into a single hex file, softdevice, bootsettings, bootloader and application. Mergehex is limited to 3 input files, which means that the complete flash image always takes 2 successive merges.
This is not a big deal, but it would seem to be trivial to extend the mergehex tool to accept 4 input files.
TIA,
Richard