Winning major tournaments has always been about when the form of the team peaks. Clearly the trend is that Portugal is playing better the tournament goes along.
I'm really not a fan of the new tournament format though - it puts too little emphasis on the performance during group stages. You're also effectively giving more incentive for teams to play for draws, which can quite effectively get you out of the group stage.
I also don't really like the fact that we are comparing the points/goal difference across the different groups. I mean seriously Portugal faced Iceland, Hungary, Austria, and got no wins. Compare them against Turkey, who also got 3 points from their group of Spain, Croatia, and Czech Republic, except they actually got a win but had a worse goal difference. To me it's a little unfair that Portugal goes through over Turkey in this situation as after adjusting for the opposition Turkey's result isn't any worse than Portugal's. I know Portugal later beat Croatia, but who knows what would have happend if Turkey played Croatia again? It's a different day and stage of the tournament at that point.