For Wagner withdrawing from Skate America means she didn't get Grand Prix points for Skate America, and her points from Skate Canada weren't enough for her to qualify for the Grand Prix Final, so she won't be there. The benefit of the doubt does not go to the skater in this case.
Each country has its own rules for how to be selected for the Olympics and European, Four Continents, and World Championships teams. If a skater has to withdraw from a selection competition, that country's rules say whether they can give that skater the benefit of the doubt.