Technically , you are right , about the timeline spliting there , not about minish cap . Because in real life , it is true when people say "If you kill a butterfly in the past , it will change the future drastically ". It is mainly the actions that changes everything . I watch this thing in the History Channel where it said that "...There are millions of Dimensions... " and "what every could of happened , did...". What is was trying to say is , like , if you had a cup of milk , and you spilled it , in an other Dimension , you didn't , and in the next dimension , you did . So that's where the saying "What ever could of happened , did " applies . So the question "Do you want to an engineer or an warrior" could just be one of billions of questions that created a new timeline . When i say "...one of billions..." i am talking about all of the questions ever asked in the Zelda series . Like "Do you want a blue or Red potion ? " or "Do you want to go to the Water Temple first ?".
But i really don't know what to say about the Connection from Spirit Tracks to Minish cap and/or an other new game yet to be released...