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).

3) hired one of the iNES developers to develop their emulator, who kept using the file-format they were familiar with.

https://news.ycombinator.com/item?id=22756156