Pinkie Pie breaking the fourth wall to acknowledge or even directly address the readers and/or the author is something of a Running Gag in FiM fanfiction in general. Sometimes other characters get in on the act, more often it's waved off as her just being Pinkie.
In The Last Airbender parody Bring Me All Your Elderly, the Animated!Characters not only are aware that they are animated (and discuss it very casually), they also leave the Animated!Universe to enter the Movie!Universe, generally blame all unexplained events either on the fanfic author or M. Night Shyamalan, read their own fanfic and comments straight off the internet, and basically suffer severe existential crises as a result. The fourth wall itself actually makes a brief appearance at one point in the story, along with a sign that says "fragile."
Mai: But for future reference, guys - try to be careful about breaking the fourth wall around Zuko, okay? He doesn't know, and it tends to freak him out a little.
Zuko: Fourth wall? What wall? Someone broke a wall?
Sweetie's Mansion: Pinkie Pie still has this ability even as a brainwashed ghost that is out to kill Sweetie Belle. Upon catching her, Sweetie gains this ability as well and unintentionally calls the author out for the direction the story is going when she's in Lotus-Eater Machine.
At the end of Paper Mario X 2: The Thousand Year Door, Link puts out a velved box out of his bag. Inside includes a ring which he uses to propose to Zelda. The very last line is Link addressing to the audience: "Can you guess what I'm going to do?"
Imperfect Metamorphosis: In a rare totally serious example, Yukari inadvertently weaponizes this against Yuuka when she reaches into her soul and generally rips things apart. This leads to Yuuka periodically taking over the narration and speaking directly to the reader, as well as adjusting her myriad plans to manipulate the established narrative.
The first hint towards this comes in a memorable Madness Mantra ("It can't be. Just words on a page. It's all paper. And not even real paper.") which Yuuka keeps muttering to herself while ignoring being pummelled into the dust by Yukari.
The Reading Rainbowverse has as its central concept the idea that various ponies are commenting on comics and answering questions. That's not this trope. What is this trope is when a reader pointed out to Gilda her blog had been hijacked by a mysterious "mod" person, resulting in the two having a bit of a tussle.
A New Order: Helios does this when speaking with the ghost of Queen Serenity. He and she both know the secret of the Time Gates (him because he read her mind) but he asks her to explain it anyway because the people on the fourth wall don't know.
In the Medaka Box fanfic World As Myth, Misogi Kumagawa recognizes when bold font and italics are used in dialogue.
Anshin'in seems to be aware of the events of the original manga.