You need FEZCofig or MFDeploy, and of course the GHI USB drivers installed.
But if you use IFU, then you don’t need any of these installed.
You could for example detect if an USB stick is connected to USB host, or a SD card is inserted.
If it contains a new hex file, you could initiate the update.
Or you write the file to the device by FTP.
Or you send it over Ethernet to opened TCP server socket on device.
IFU is more work in the first place, but finally it makes updates more easy, because no drivers are needed on the updating computer, which is in some scenarios not necessary either (USB Stick, …).
but IFU bears one risk:
If you get a bug into the IFU part of your device software, that prevents updates, you can not fix this bug with an new IFU update. You need to update these devices with MFDeploy/FEZConfig then one time.
I think this happened to a Palm device once. To be able to apply any updates, the Palm owners had to open the case and push some internal buttons to boot it in loader mode, and then use a special software to update it.