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Of course, this was not a new concept for the franchise as a whole, since the notion of "Hackers" and "Programming" has already been used even in anime as demonstrated a few times in Digimon Adventure and also in Digimon Tamers.
Some time ago @TheWindragon24 drew my attention to discussions about how Digimon is currently being managed. Well, I am not talking about the quality of products, after all I am not able to buy most of them (mostly games, and that's because I save during a whole year)
At the time of Digimon Savers, that expanded the story of Yggdrasil and the Royal Knights, we have the explanation that Yggdrasil is a God and that is why he is everywhere and nowhere, without a form that can be observed, only felt.
Another explanation was given in the following episode, giving more details on what the distortions really would be.
It is when it is explained that temples and shrines were created to prevent "Demon Gates" from appearing, portals that could lead to apparitions of evil spirits from another world.
Then, distortions started to happen in the Real World and is when Miyako starts to wonder about why Digimon are appearing in Kyoto, and is when the Digimon and Youkai relation was first explained in the anime.
This started to be speculated as the result of the weakening of the mysterious forces that protect the Digital World. So we can see this connection between distortions and the world losing its balance.
This concept would later be used in other products, such as Digimon Xros Wars, Re:Digitize or Cyber Sleuth where the nature of the Digital World being superior to our "real" world was made very explicit
Of course, Digimon Story Sunburst / Moonlight also continued with this, explaining more of the Servers and also reusing the notion that each copy of the game can be interpreted as a "Different Server".