I had saved this article for later reading as I was interested why researchers wouldn't "know why this game works". I finally got around to reading the referenced scientific paper and I was disappointed to find that this news article is very misleading, but pleasantly surprised by what the paper is actually about.
The researchers consider themselves digital archaeologists - reverse engineering code and techniques from an Atari game. One of the things they looked at was the maze generation algorithm which uses a 32-byte lookup table. After trying a few things to see if the table was following some patterns, they conclude:
"Our conclusion is that the table values were manually chosen, or manually tuned, by the maze algorithm designer."
There is nothing magical about this algorithm, as the researchers themselves already conclude earlier in the paper:
"This is a “make-break,” and acquiring these allows the player to make a new piece of maze wall or, more importantly, remove an existing piece of wall."
"The fact that make-breaks are needed speaks to the algorithm used for maze generation (...)"
It is important to note that the paper spends a lot more time on the history of the game (as you would expect from archaeologists). This is also why they contacted the original developer to understand how certain code came to be and what provided the hilarious quote that is featured in this news article.
In short, for those interested in the history of Atari 2600 game development, I would highly recommend the paper, but don't expect to find any unsolved mathematical mysteries.