Miyamoto has also neglected to address the fact that certain characters have the exact same name as the species to which they belong. That guy's standards are jank, Nintendo canon is like saying an apple is a banana. Clearly that doesn't make sense, but they'll tell you it's true anyway.
If you're talking about Toad, the whole "Toad named Toad" thing has gotten way out of hand due to all of the inconsistencies between the fan **** (which was where the concept actually came from; there in reality
is no major Toad named "Toad", but that's a discussion for a different thread) to the point that
every major Toad that shows up now is "Toad", except when they're not (i.e. Captain Toad was "Toad" to people when Galaxy and Galaxy 2 came out, but once 3D World came out, now the blue Toad is "Toad" instead of "Blue Toad" from the NSMB games and Captain Toad is someone else.
).
That's stretching it--in the same interview you got that from, Miyamoto didn't imply that--only that Dr. Mario is not canon, like all the other Mario spin-offs. He singled out Dr. Mario as an example, not an exception to, the idea of non mainline Super Mario Bros. games being seen as little more than side activities for the plumber.
It's more than just the interview. It's the Dr. Mario franchise
itself.
Dr. Mario is supposed to be this guy that's working day and night to develop miracle cures (with the cure for the common cold being elusive) and wipe out infectious viruses, yet has time to work part-time as a plumber and save Princess Peach on a regular basis?
And host extracurricular activities?
And speaking of Peach, she's supposed to be
right by Dr. Mario's side the whole time as a nurse? How is she able do that
and govern her kingdom (though admittedly she's kind of terrible at that...)?
And don't get me started on Wario's involvement in the franchise. No, Wario's not the problem. It's that Dr. Mario's world is filled with enemies from Wario Land 3,
including it's antagonist, Rudy the Clown. Except....all of those enemies are from the Music Box World, and weren't enemies at all, let alone Rudy's
minions. They were the citizens of the world transformed into monsters by Rudy as a last act of defiance before they sealed him away. They only went after Wario to
stop him from reviving Rudy. And Rudy himself? He's supposed to be larger than life. He was the
background in his fight with Wario.
In Dr. Mario 64, he's freaking
puny!
And apparently has a mountainous jugular.
But the worst part of this is....Rudy is supposed to be
dead. Wario killed him! And it's not like when Mario "kills" Bowser whenever they fight; Rudy was Killed Off for Real, just like many other of Wario's foes. Why is he alive? And why is he outside the Music Box World?
And then there's the fact that swallowing Megavitamins apparently has the same effect as grabbing a Metal Cap (Mario) and being bitten by bats (Wario), but I'm not going to delve into that too much.
To top it off, unlike other side Mario series, barely anything from Dr. Mario is featured in other Mario titles. Only the Virus enemies in two of the Mario & Luigi RPGs, and they're not microscopic and have to be killed by pills, they're Goomba-sized.
As well as special Virus items in the Mario Kart Arcade GP titles that are
based off of the Viruses (specifically the Blue Virus).
You can use the "it's not canon" excuse, but that only means it's not canon to the
Mario franchise. Dr. Mario
is a franchise all of its own. It's not just one game, it's FIVE (not counting things like the GB Dr. Mario, Dr. Mario & Tetris, Vs. Dr. Mario, Dr. Mario & Puzzle League, etc.), though the last game starred Dr.
Luigi instead.
It has its own canon. It's own universe. An alternate universe where Mario is a doctor, not a plumber.