Although I see how you could think the Nipperkin thing is totally random and not story-related, I see it as a way to get familiar with the places and people on the Island.
And well the story hasn't really /started/ by that time.
However I think the fact that the puzzles you names were from the first and second chapter might mean that they got better at it. I definitely think that the chapters got better and better (although my fav is 4 and not 5), so I'm not sure they really need to be told the first chapters weren't as good. They improved on them so they must have noticed, right?