I'm actually not surprised, so I'm a bit surprised others are. If only I knew about PM earlier, I would've tried to mention the warning at the very first tourney entry. That it would likely only last until there's official sponsorship. Unless we saw the likes Capcom and SNK allowing mods and/or hacked versions of their games at tournaments they sponsor, then there's a chance it won't get allowed. I'm sure, (or at least I HOPE) people were mentioning something about this by the time Nintendo decided to officially support the games. I would've repeated this warning since 10 years ago, or so. Alas, stuff like Street fighter, KOF, Guilty Gear, had my time, back then. I was unaware of the Smash community, at the time.
Still, the bright-side about Smash 4 is the amount of built-in modifiers to what effectively affects the game engine, with no additional stuff pushed in. Someone could adjust it by adding those modifiers to the characters and it will still be Smash 4, as far as Nintendo is concerned. And while, I still have confidence in the post-release support for it, the fact they threw so many options in there really helps, in the long run.
While I don't hate PM, whatsoever. I would've been for allowing it, but with the warning about official sponsorships and what they mean. I also understand the concern of companies which sponsor events and want to see the games "For which they personally have code version control" represented. Not games, for which version control is completely out of their hands. That's putting their own responsibility, reputation, and representation behind the efforts of complete strangers. If the likes of other major Fighting game companies don't want to, I don't see why Nintendo would be different. Especially now they have the efforts of a known fighting-game company behind the latest project.
People old enough would remember that even the likes of Street Fighter had some pretty nifty modifications, as well. But when official tournaments got in the picture, only official SF games were allowed.