Because Nintendo wanted to sell those upgrades instead of someone patching them into the save file?
It’s really insane if this story is true.
You use a program to create a file. You modify the file that you created with the program using a different program. Company sues you claiming they own the file that you created with the program you legally purchased.
I wonder what tool chain Nintendo uses internally. Could Notepad++ sue Nintendo for modifying a text file created by Notepad++ without always using Notepad++? They’re unfairly cutting Notepad++ out of competition by using vim on txt files originally created with Notepad++ then profiting on the results by selling games that used the modified txt files after compiling them into games.