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About the author's childhood and teen days

He was 2 years when he was returned to the Nakajima family after his parents official divorce. He has no memory of his mother. In some of the old letters that narrate this episode of his life it's quoted that he whined "where did kaachan go?" 

He was raised in his early years by his grandmother, aunt, and cousins at his father's hometown. His father took care of him when Atsushi was 5 years old.

Atsushi lived with his father and two step mothers during his childhood, but he did not get along well with them.

During his childhood he moved constantly from cities, so this developed in him a lack of sense of nostalgia for his hometown.

Katsu Konya (his 1st step-mother) was a very strict woman, some memoirs of the author mentioned her tying him to a tree as punishment and that he did not received snacks from her but only a caramel. 

During his teen years he got beaten by his father due his rebellious behavior and despise towards his 2nd step-mother.

Some studies consider that not knowing his mother and the distance between him and his father caused Atsushi to grow distrustful of the world. This may be why Atsushi's written works showed a feeling of  "uncertainty of existence" too.

Personally, I believe that the quote is not trying to imply something grotesque per se. I'm aware there's a theory going around TikTok in which the interpretation of this quote has been twisted into something else, but skimming the manga and even watching the anime we get to watch the Headmaster constantly reminding Atsushi he is an abandoned child who may or may not be in fact thrown away by his parents and taken in by the orphanage’s staff,

When child Atsushi is seen crying in those flashbacks he is reminded that he has no rights for crying, because again, he has no parents who can be accountable of him

Some panels from the manga also show the Headmaster reminding him that he has no right of having belongings or a place in this world too, because according to the Headmaster he’s a forsaken child by everyone

Considering one more time the quote: "Compared to what your parents did to you in your infancy, this doesn’t even count as violence”, it feels more like a reminder (from the headmaster's perspective) that there's no other bigger act of abuse and violence towards an infant than "abandonment" from their one very own parents. They were supposed to provide infant Atsushi with a place to call home, love and care rather than just throwing him away in the garbage (as the Headmaster mentioned, but still nothing of that is completely confirmed tho).

Taking into account the author's childhood and going back to each time Atsushi remembers the orphanage and the Headmaster, it feels more like the last one justified the abuse imposed on Atsushi merely on the fact that nothing else can be worse than being thrown away and forsaken by those who brought him into the world. 

Asagiri Kafka commented in that new interview that he reads the written works from the authors as well as he takes inspiration from the authors themselves. As I see it, Asagiri experiments with the work and life of each author he included in bsd and he has this sort of "what ifs" so I don't doubt he has used some nuances of Nakajima Atsushi's life. This may be why he created a torturous past for the character by adding the coming up with the concept of an abandoned child Atsushi Nakajima, a little Atsushi who lived through hell at an orphanage that abused and neglected him based on irl Nakajima Atsushi's early childhood and teen years, where he was in a way abandoned by his mother after his parents's divorce, raised in a very strict environment by his first step-mother and living in a huge distant from his father.