I did quickly go through the manga, with the help of the fanwiki, to see how much that "Atsushi's orphanage headmaster visions have been caused by Q" twist holds up (as sometimes, new plans come up as you write, especially if your series is over 10 years old)
In the first chapter, Atsushi has a flashback of the orphanage staff kicking him out, but they do not have individual identities. The first apparition of the headmaster as himself is when Atsushi is under the influence of Dogra Magra, in chapter 25, "Q":
His next apparition is in chapter 28, when Atsushi is being held in the Moby Dick, right before Lucy comes in and chooses to help him (note: that scene also compares Atsushi's abuse is compared to another person's, Lucy's.)
After that, there's chapter 39, "Portrait of a Father", where Atsushi doesn't hallucinate him, but we learn about who the man was to Atsushi, and witness his funeral.
His next hallucination is in chapter 52, at the very end of the Cannibalism arc. He explains to Akutagawa that the headmaster has been been haunting him less since (the final fight on) the Moby Dick, but has been silent since the funeral.
There are a few more mentions of the headmaster that I haven't mentioned, but a very notable one is that Atsushi saw becoming stronger and his upcoming fight against Akutagawa as a way to free himself from the headmaster's influence, much like Akutagawa saw it as a way to gain Dazai's approval.
I don't think we see Atsushi hallucinating the headmaster after this until chapter 122, but the Dazai hallucinations start showing up in chapter 63, so really not that long after the previous one. The next Dazai ones I could find were in chapters 78, 105 and 121.
The conclusion is therefore that Atsushi hallucinating the headmaster has been a very active and purposeful part of his journey as a character since very early on. It started manifesting after Atsushi's breakdown while under the influence of Q's ability, and it's taken various approaches as Atsushi faced different struggles, but it's always been there.
While wearing Dazai's face, the hallucination was given more credit in Atsushi's eyes, but its words were barely less sharp and hurtful. However, they did tend to push Atsushi into acting, rather than cowering and giving up.
We're seeing Atsushi heal in real time, no matter how messy it is, and I'm so proud of him.