Yep. They even have the final 'double ideas' where two bonuses are listed as separate, but you can't actually have one and not the other. There's essentially no reason in EU4 to split the final idea from the bonus idea or the national ambitions from their final national idea. It looks like this is also going to be the case with the military traditions.Kind of seems like EU4's ideas a little.
Now they could actually fix this problem if they let you pick the traditions in any order, or at least not entirely linearly, and the final bonus was instead what you got for completing the set. Which is why Stellaris traditions do make sense to include a final additional bonus for completing the set.