This is a very special bootloader which can be flashed in any bootloader version BUT to flash it your Hermes must be SuperCID first. It allows flashing of unsigned code via the 'lnb' command, and probably NBF files via 'wdata' command (still untested).
In addition, it seems you have to use it if you want to combine ROM parts from different shipped upgrades, handy if you want to the latest OS, but don't want to lock your bootloader.
Device will reboot after this, with bootloader 1.04 on it.
Benefits of using MFG bootloader
You can flash unsigned code (Cooked ROMS, etc..)-(WARNING: COOKED ROMS STILL PRODUCE BAD BLOCKS RESULTING IN BRICKED DEVICES)
You can choose which ROM parts you want to flash: SPL, MainSplash, SubSplash, OS or ExtROM
It allows you to flash extracted-radio ROMs (ONLY if on Radio BL0107)
Downside of using MFG bootloader
You can't do a full ROM upgrade in NBH again, you need to flash 1.04 first
If you type an address wrong when flashing you can brick your device
It has not been much tested yet#
With Hard-SPL, it's essentially pointless to use
BootLoader 1.01 MFG HowTo
As said, this bootloader allows you to flash unsigned code, this means you can combine ROM parts from shipped upgrades, or even make your custom parts. To extract the contents from a shipped upgrade, unrar the exe file, and use NBHExtract.exe with the NBH file inside the shipped upgrade package.
WARNING: ONLY FLASH OS.nb EXTRACTED FROM A NBH, DON'T FLASH ANY OS.nb YOU MODIFIED OR COOKED OR YOU WILL END UP WITH BAD BLOCKS IN NAND FLASH.
Cooking OS.nb
It is possible to cook hermes OS.nb with mamaich IMGFS tools, but this is still very highly experimental and can brick your device if you don't know what you are doing (REALLY, PRODUCES BAD BLOCKS IN NAND!).
Please follow this thread on the forum if you are interested in cooking ROMs:
http://forum.xda-developers.com/showthread.php?t=289377
Flashing an extracted radio only
It is not possible to flash an extracted radio with MFG bootloader, you have to first flash a 1.04 bootloader using 1.01 MFG. Next, flash desired radio. Then flash back to 1.01 MFG.