Sure Nintendo might have just downloaded the rom, but they may have:

1) just concatenated the prg and chr roms and added an iNES header so they could validate in third party emulators. (Likely extra helpful for games where they were developing anti-epilepsy patches, since third party emulators have some really nice debugging tools.)

or

2) Used a third party cart dumper that adds the iNES header, because it was faster and easier than setting up a 3.5 inch floppy drive to try read the original rom from the archive. (And much faster than retyping in hex dump printout from the archive).