UThis post from xda sums things up brilliantly, replying to a question someone posed about flashing the new mj5 on the old bootloader:
"You can flash with odin MJ5 and you flag shoud remain 0x0, but you will be stuck with new bootloader.
Problem with rooting ROM with new bootloader is solved, so you can root and still not trigger knox flag if you folow guides here.
But, if you try change bootloader or flash custom recovery or custom kernel you will trigger knox flag.
So it is better solution wait CWM version with custom kernel and with old bootloader because you will be knox free and have more opportunities. Combination of old bootloader and custom kernel are obligation, because old bootloader and stock 4.3 kernel symply won't work (wifi and sound problem).
So this new version still does not allow you to use custom recovery and stay Knox free.
Seems echoe rom is the best option for now for those of us on old bootloader wanting to try 4.3, once the updated version with the new stock kernel is released....