Just because they don't talk about it anymore doesn't mean they threw it away. It may simply be irrelevant now since Mario lives in the Mushroom Kingdom or they may not wish to bring it up since, as established before, there is no official canon. This simply means that Nintendo does not spoon-feed us what to accept or what to disregard. So I don't see the problem if I want to include this in a comprehensive timeline of the entire Mario franchise.
But my main point is that Nintendo never denied that Mario is from Brooklyn. Even if Nintendo of America doesn't talk about it today, that doesn't undo the fact that they have before through their Mario media.
You keep disregarding the Brooklyn story since it is not mentioned in the games. I think this brings up the issue of authorship.
When Miyamoto created this fictional world, he obviously becomes the author. He has the authority that establishes the characters, how the world works, etc. Since he made this fictional reality under contract with Nintendo, Nintendo owns the rights. When Nintendo offers these rights to a third party like Valiant or DiC, they grant them the authorship to make a statement about that fictional reality. But being the original authors, Miyamoto and Nintendo have a greater authority. So although Princess Peach Toadstool has appeared with red hair in some media, Nintendo's official character art takes precedence over that. But the issue of Mario growing up in Brooklyn does not contradict what Miyamoto has established in his higher authority.
Yes, we see the babies delivered to the Mushroom Kingdom, but how did they get there? Where did the stork get them? Could they have possibly been born elsewhere and delivered somewhere else? Did the babies move and grow up somewhere else? These are simply gaps in the timeline free for the fans to speculate and theorize until a higher authority makes a statement.
So to answer your questions...
...then why isn't Bowser a T-Rex-turned-human in any Mario game?
He isn't because there is no way to reconcile the story of the live-action Mario movie with the timeline from the games. The movie makers had a degree of authorship to contribute, but they instead made their own version that blatantly contradicts the source material, the higher authority.
I do not believe that the comics/books/cartoons make such a contradiction, so I see no reason to disregard it in my comprehensive timeline of the entire Mario series.Why didn't the events of SMW involve Peach wearing Luigi's clothes?
Not an issue. The
Super Mario Adventures comic book was not a retelling of
Super Mario World. It was its own story.
By the way, when I mentioned that it has been established that Mario is from Brooklyn in an actual game, I was referring to
Mario's Time Machine, not
Mario is Missing.
Maybe one day I'll post my comprehensive timeline on the Mario series in this forum.