A correct ROM packaged using the emulation community's standard file format will exactly match a pirated copy. There is no story here. After the article came out, Nintendo even created their own incompatible ROM packaging format just to spite that article.

What this article is about is that Nintendo used a format standard in the emulation community for the ROM, it's possible they downloaded it but it's not like there's some "downloaded from ROMZ-ZONE.RU" watermark in there. It has been revealed in leaks that Nintendo has an internal ROM vault of pretty much everything ever released on their systems.

Also how WarioWare: Smooth Moves shows their in-house developers using third-party emulators to source graphics for their first-party nostalgia bait: https://tcrf.net/WarioWare:_Smooth_Moves#Punch-Out (not said derisively; I love WarioWare!)

There’s still no proof they pirated the ROM

They were only "caught" using the .NES header which is a public standard that many NES emulators implement. There is no evidence that they used a pirated ROM.

If someone breaks into a warehouse and makes off with a pallet of cartridges, and then those carts are recovered, would it be strange if Nintendo resold those carts? It's their property at the end of the day.

Aside from that thought exercise, like many "internet facts" this one also might not be true, and repeating it doesn't really help either "side."

https://medium.com/@AberrantWolf/mario-illegal-roms-and-medi...