Overall, Rex is the core protagonist among the three main characters. That's what essentially is being said. Neither the first game nor the last game to do so. That's why he was considered among the moveset first. Basically in the way that Pokemon Trainer is compared to the other three Pokemon(giving commands and all). Unfortunately, that wasn't entirely plausible due to limitations. That, and I think Rex was supposed to take action beyond giving commands anyway? I forget.
But anyway, Nintendo's involvement in the DLC made sense; they're the ones who went to Sakurai to get it started. That, and Sakurai himself is getting older. Trying to maintain all the decisions is pretty damn stressful. Nintendo helping more relieves that a bit. Finally, do note that by default, a lot of decisions do need to go through Nintendo. They don't fully own Pokemon, but more importantly, some stuff Sakurai can't do with them even when being given the hard decision(sometimes) to choose who he wants overall as a character. He can only pick so many costumes. 3rd party licensing is a given on its own, but let's also note how particular they can be about costumes and representation. As Sakurai isn't the owner of Smash itself, Nintendo will have a representative there since they literally own the franchise. It makes sense they're reasonably involved. It's their game. They would always be involved anyway.
As for them helping with the roster more, it's not surprising anyway. As I said a bit before, Sakurai's getting older. That, and while Sakurai sees it more as a celebration, Nintendo is going to see business as part of it a tad more. It's their product at the end of the day, so that makes a lot of sense. Even then, it's clear they've still given him tons of control. It was already noted that if a character couldn't work, Sakurai can say "no" to it. It's implied he never said no, but all he said was nobody in Pass 1 was rejected for moveset issues. We don't know enough about Pass 2, though. Beyond Rex not being able to fully be utilized, respectively).