It wasn't supposed to be taken as canon. That was the whole point. The Wachowskis essentially confirmed that at the end. PON allowed you to play through all the good parts from the movies, but it also allowed you to take a path different from what Neo did. Yeah the Chateau part was pretty crazy, but the purpose of the game was to have fun, not to simply duplicate the movies.
For example, you can escape Metacortex and meet up with Trinity and her motorcycle, instead of letting yourself get caught by Smith. Or you CAN let yourself get caught by Smith if you prefer, doesn't matter. Instead of just flying away at Debir Court, you can kill all the Smiths. Instead of having Smith use your head as a crater-creator, you can do that to him instead. And then of course, the final battle was nothing like the movies.
So although the game wasn't perfect, there were plenty of awesome moments. Don't discount it just because its not canon.