Looking at a decent number of articles about the 1954 world cup, none of them talk about why the tournament had the strange format. Some only mention the format and note how strange it was comparing to current-day format. But that being said, the format is strange to us because we've had a format that hasn't changed much in many years and is very symmetric.
Let's take a look at the previous tournaments:
- The 1930 world cup had 13 teams, hard to imagine having odd number of teams now a days.
- The 1934 and 1928 tournaments had no group stage, all matches were knockout matches.
- The 1950 games had 2 rounds of group stages. The 4 winners of the initial group round played another set of round robin matches to determine the champion.
So although the 1954 tournament had a weird format, there had been no agreed upon format yet. All world cups till then had a strange format with today's standard. The hosts and FIFA were still trying to figure out a "fair" format. Traveling was much harder back in the day - think of having teams travel to Uruguay back in 1930! Also as the tournament gained more and more popularity, and with the rise of broadcasting, having more matches and teams to increase revenue became a goal for the organizers.
Nonetheless, the format was criticized, eventually leading to a format we currently have.
All that aside my guess is the mentality was that the best team should win the tournament, regardless of the format. If I had to speculate why the knockout stage of the tournament was held that way, these are what I can think of:
It guarantees blockbuster match ups
- Currently, the group winners play another group's runner up. By forcing the group winners to play each other, you guarantee that you get higher anticipated/quality match ups. Under current format it's possible there are no group winners left in round of 8 or after. Again, if the best team is supposed to win, format doesn't matter.
It makes knockout matches more intriguing
- Teams playing each other would be playing opponents of similar quality. You could argue the current format benefits top teams as they don't tend to play teams of their quality or better till the very end, while weaker teams have to pull an upset match after match to get deep.
It exhibits higher fairness for weaker teams
- By matching up teams of similar strength, a weaker team is given more chance of getting to the final and winning the tournament. After all, West Germany's win over Hungary was a major upset. West Germany was an unseeded team in the tournament and they had already beaten 8-3 by Hungary in the group round.