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Seems like you didn’t read the article. His job was updating the website not modifying objects. Also, your argument is wrong on its face - the company he worked for modified objects to allow them to commit piracy. If you modify a stick into a shiv and stab someone, you won’t be arrested because you “modified an object that you own” – you’ll be arrested because your modified object was then used in a crime.
Now, whether intellectual property laws are morally just, whether Nintendo are being assholes, whether he should be afforded free healthcare rather than having his income garnished to a private multi-billion dollar company, etc. are different issues
Not to stretch the metaphor too taught, but in this case the guy going to jail was the guy who runs the social media for a business that sharpen sticks for folks that don’t know how to do it themselves, not the guy actually doing any stabbings.