You don't seem to be understanding the difference here. I'm not sure how much more clearly I can explain it, but I can try.
Year One era stories (Legends of the Dark Knight, Dark Moon Rising, etc.) are self-contained stories set in the early years of Bruce's career. The purpose of these stories is to flesh out Batman's career with events that happened during this period. These stories do not exist to set up for future arcs or threats. They are simply entire stories set in the past that tell a complete tale (beginning, middle, and end) that adds more stories to that era of a character's history, but does not modify it significantly going forward.
Snyder and Tynion often tell stories in the present day that use flashbacks to the past to introduce a new threat from the shadows of the character's history. These arcs are set in the present and thus are present day stories. The connections the writers create to the hero's past are meant to establish the new villain as a threat. Forcing the character into the character's history makes the villain appear to be a bigger menace and is an easy way to introduce a new threat without building it up. Rather than introduce the character in the modern day and build up their reputation, writers like Snyder insert them into the past and make them an large part of the character's past to make the threat seem important. This story begins and resolves in the modern day. It is a modern day story that creates a fictional history to give it articial weight. It is not a story that is set in the past or intended to flesh out an era of the character's history.
You seem to view these stories the other way around. You view these stories as attempts to flesh out the character's histories that have repercussions in the modern day. In reality, it is the other way around. In order to establish a new and menacing modern day threat, Snyder and Tynion modify a character's history to add weight to their modern day story.
There are ways to create new, interesting, and menacing threats without having to stuff them into a character's history. Most of Batman's famous rouges, including Joker and Ras al Ghul, were introduced in the then present day without writing them into Batman's origins. Snyder's route of conjuring new villains out of the past feels cheap because the reader is expected to believe that these signicant events happened in the past without any mention or additional altercation happening between then and the present. It feels cheap and unearned to tell the readers to accept that something happened in the past with no indication before that the event had ever happened. This is why I call it a shortcut.
In small doses, this might have been fine. Black Mirror is one of my favorite stories, but looking back, it does seem to use the traditional "threat from the past" mold that Snyder overuses. (It does however use a character that had been previously introduced rather than inventing a new one.) I accepted the Court of Owls change to Dick Grayson's history at the time despite disliking it, but after so many similar stories written by Snyder and Tynion, for character including but not limited to Kate Kane, Cassandra Cain, Alfred, Batman, Dick Grayson, and Ras al Ghul, it feels like part of a cheap story template than a meaningful attempt to enrich the character's history. That's because that is exactly what this type of story is: an easy template to quickly establish a modern day threat that carries weight to it. There are other, more challenging ways to build up threats, but rather than add variety to their storytelling, Snyder and Tynion reuse the same basic plot structure over and over and over again.