There are many examples of teams undeservedly going through based on refereeing decisions alone. Liverpool 2005, Barcelona 2009, Chelsea 2012, that's without even looking through the years.
The width of a post or crossbar putting you through or out isn't skill or merit, neither is a deflected shot, neither is missing key players at the wrong time. You obviously don't win if you are not good or are not playing a system that gets results, but there are too many variables in knock-out football to talk about consistent deserving winners. The team that wins it takes advantage of the circumstances in the game.
Another thing, look at all the recent winners who weren't even league champions. It's a tournament which identifies the team who are most opportune, best or deserving doesn't really matter.
Take the Sturaro moment as a case in point, that is a mixture of skill, determination and luck, that header from James could go anywhere. That is a super slow-motion image and he is just putting his foot up and hoping for the best. Sometimes that's all you do in sport, who decides whether something is deserving or not?