Determining 2nd and 3rd place from a single-elimination bracket

An example is the knockout rounds of the World Cup. The possible teams that can make the podium are determined by the initial placements of all the teams. For example, in the case of the recent World Cup, it would have been impossible for Spain and Austria to both take the podium. Likewise, if Austria and Argentina were to swap their initial positions (and we assume that the match between Spain and Argentina would be the same as in the finals), then Argentina wouldn't be in second place. So to me, the overall "second-best" team of the World Cup is either Austria, Portugal, Belgium, France, or Argentina. We can go further and say that the overall "third-best" team is one of the previous 4 teams, plus Croatia, Senegal, USA, Sweden, Paraguay, Morocco, Cape Verde, Egypt, or Switzerland. (This is, however, under the rather big assumption that every team's skill level is "fixed" before the tournament and the outcome of any match is determined by comparing skill levels.)

Of course, this is not limited to the World Cup, but to any competition that uses the same tournament bracket to determine second and third place. And I know that it ultimately doesn't matter most of the time since luck is usually involved in any tournament. And I know that sometimes the players/teams will be deliberately arranged in separate parts of the bracket to avoid early matches between two strong opponents. But it still rubs me the wrong way, which is why it's sorta my pet peeve. There are flaws in any kind of tournament structure, but I can't help but think about this flaw in the single-elimination bracket.