Great application !
Files identical (same CRC) from unbranded to branded roms:
All the remaining files are different, inclueding the flash but that is obvious.
(amss.mbn, amsshd.mbn, appsboot.mbn, Flash.bin)
I guess we have to compare the unidentical mbn files to find out what prevents the unbranded roms to work in phones with branded NVs.
Then if nothing is conclusive we will have to check the flash itself.
mbn files seem plain/uncompressed binaries.
In fact I believe the CID checks are performed by amss.mbn which seems to be somehow the true bootloader (It is a true ELF binary and likely the very first to be running)