Surely lots of people make house rules to certain games, no? And isn't that a game "you weren't intended to play?"
My buddy and I still play the 17-year-old Super Mario Kart regularly, but the game's evolved with a ton of house rules. Some exampes:
1 - If you get a ghost, you have to either steal the opponent's current item or the very next one, but you can't just hold onto it waiting for a red shell.
2 - If you get a banana, you can yell "GAME!" and the other player has to stop. Then you position yourself, and try to hit him by throwing the banana.
3 - If you have one hit left, your opponent has all three, and you get a green shell...
This wasn't the game the designers necessarily had in mind, but it's the game we like. Ghosts are too powerful. Bananas are too boring. So we tweak the rules.
TFA mentions Easter eggs rather than house rules. Easter eggs just can't be what they were before; the internet makes it too easy to learn everything about a game. There's no way the new Zelda will have a secret room that nobody knows about for years, but ~10 years went by before I found out about the secret room in Zelda for SNES. You just can't have secrets like that in popular games anymore.