I reckon, from past Iwata Asks that Nintendo doesn't really come in between outside development cultures like that; their supervising effort is to pull out the best game possible and for that they might demand stuff, but it's in the train of thought of keeping the core idea intact or adding to it.
With Xenoblade, Takahashi was actually ready to give up some features in order to comply with deadlines (and the fact the team was getting tired) it was Nintendo that maneuvered it around. Also, Monolith usually did games as a whole with resources going back and forth so having a estimated completion date was hard and Nintendo insisted that for Xenoblade they worked by sections, which they said helped a lot actually. Other than that, the only compromise Nintendo made them do was that they focused on plot concept before, and gameplay came as a secondary and with Nintendo they have to flesh out the gameplay (happened on Soma Bringer, first game they started work on without having a plot).
Nintendo doesn't want these studios to do the games they can do in-house. Thankfully.