Ok so I've found out why, for anyone that could find this thread later on, with the same issue. It is far simple as Skyscrapper, at the time of this posting, does not support Famicom and Super Famicom as a platform. Maybe in a futur update? Maybe never? We'll see in time.

For now I've placed my Famicom in my NES rom and Super Famicom in my SNES folder and did the scrape. Then I moved it back to the famicom and sfc folder respectively, including the gamelist.xml and the media folder.

It's a bit of a hassle, but it get the job done.

URL to the supported Skyscrapper platform :
https://github.com/muldjord/skyscraper/blob/master/docs/PLATFORMS.md

Scrapers