Only way it leads to meaningless games is if the first team to play twice, loses both games. Then, the last game doesn't matter.
For example you have a group consisting of US, Italy, Cameroon. First game, US beats Cameroon. Second game, Italy beats Cameroon. Now, Italy vs US is only for seeding.
But, if the opposite happens. Cameroon beats US, then Cameroon beats Italy, then the US-Italy game is huge.
I did see a side article that states to make sure every prelim game is meaningful, the winner of the first game of the group should play the 3rd team in the next game. This way, you won't have to worry about the first team playing twice, to lose both, thus making the last game meaningless.
Yes, the last game would be meaningless in terms of going through, but seeding would probably be pretty important. Assuming all the 1 seeds get matched up against the 2nd seeds, you want that #1 seed for the knockout round