Dr. Mario is described as Mario as he appeared in Dr. Mario.
Toon Link is described as Link as he appeared in Wind Waker.
Samus is described as Samus without her varia suit.
Magnus
(for example) is Magnus, if Magnus was an assist trophy and a playable character there is no real "justifible" reason as to why he can be both. It really shouldn't matter, but since the game does these things where characters are removed from the background when they are in battle I think it makes sense that this trend would continue.
As for Brawl with Captain Falcon, that was Brawl. This is Smash For, ideals change over time.
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And yes, we don't know what he really thinks unless someone asks him. Till then, we can only speculate.