They can't control what people do. If they gave permission or not is irrelevant because they're trying to shuffle PM under the rug. Here's an example I used in
another thread:
That example isn't remotely realistic. The point of IP laws like copywrite is to prevent people from inappropriately earning monetary profit from someone else's work. The litmus test over whether or not a violation has occurred has been, historically, whether or not someone is charging money / earning a profit.
Over the last 10-15 years corporations have been lobbying for legislation to blur that line, for the purposes of making it easier for them to prosecute piracy. (i.e. downloading games for free rather than paying for them). The bluring of these lines is what put PM in a legal grey area.
Still, PM clearly wasn't promoting or enabling piracy, and there's absolutely no reason why the existence of PM, as they had set it up, would pose a realistic threat to anyone's trademark or copyrighted work. If PM had the funds to fight a lawsuit, they'd have a real chance of winning.
That's not to say the PM team's decision was irrational. They don't have the funds to pay for a legal defense in the first place, and the downside risk of losing the lawsuit is way too severe to warrant taking that risk. But there's no reason to be charitable to Nintendo here. If they really were about to throw the book at the PM team, they weren't doing it because of any real harm to their product, they were doing it because of their f--ked up pride. They were pissed that PM was getting as many entrants as Melee, and got even more pissed off when PM started delivering new content.
It's a shame the PM team can't afford to fight this. Like I said up-thread, if this actually happened, it would have been a public relations disaster for Nintendo. As it is now, I've sworn off them. They're dead to me as a company.