Were any of the The Matrix movies released with extended editions?

There definitely are alternate versions. Right now, I'm watching Australian YouTubers 'Nics&Nacs' react to The Matrix and I'm watching a bathroom fight scene where Morpheus knocks Smith's sunglasses off with a headbutt, provoking Smith to return several hard headbutts. This is an extended scene. I've watched the theatrical version in Europe on VHS and on the Ultimate Collection DVD multiple times. This scene was not in them. In the original European theatrical version, it just cuts from Smith on the ground wearing his sunglasses, to him rising upright with his glasses magically vanished. I always thought it was a continuation error. I had no idea until now that a scene existed that show Morpheus knocking his glasses off.

I have the Ultimate Matrix Collection, and I can confirm that extended versions don't exist for any of The Matrix movies.

The collection comes with several DVDs, one of which in The Burly Man Chronicles, which contains many extras and interviews with people who aren't in the movie (such as critics, scholars, etc).

The link you provided is simply a forum and fan speculation about the Ultimate Matrix Collection.