After that you have the warning "A firmware reconstruction is needed to get your Mac Pro fully working."
The MP51.fd is not a complete BootROM image, it's a generic partial image specifically crafted by Apple to be used for EFI upgrades via efiflasher. It's created without the NVRAM volume and just a partial MLB sector to not mess with any of your Mac Pro serials/hardwareIDs.
Flashing it to the backplane makes your Mac Pro completely unserialized, without any hardware IDs and without the hardware descriptor. The MP51.fd is just enough to boot a Mac Pro, but you won't have any serialization/hardware IDs and consequentially no iCloud/Messages/FaceTime logins since these depend on the hardwareIDs to id your Mac Pro with the Apple services.
Btw, you can't flash a MP51.fd and serialize the backplane with BBS, there are lot's of other hardwareIDs other than the System Serial Number that BBS don't add to the BootROM. A blank board bought from Apple only won't have SSN, but all other hardwareIDs, the hardware descriptor and the MLB sector are already present inside the NVRAM volume and MLB sector.
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