Being totally honest I find it kind of odd in a way that they really have such strong issues with it just from the perspective of gender itself in a vacuum separate from trauma.
I get that the trauma's there but because this all started in prepubescence he shouldn't have been strongly psychologically male to begin with. Kids barely have a defined identity at that point to begin with let alone one that strongly adheres to their gender expression. Like at this point she'd been a girl longer than she was a fully aware/conscious person back as a boy.
Though once again that's in a vacuum which excludes the assault-based trauma and caring far too much about being a not even really all that bad kid.
Really when it comes to her development as far as her hangups I hope she realizes at some point that they did more damage to her than she ever really did to them and just stops being sorry about the inconsequential things she did during early grade/primary school.
Because they really did do worse as in chapter 38/39 the video they saw actively had a negative effect on Akira which implies if not outright showcases genuine sexual trauma from that incident back when she was 7.
heck, now that i think about it, maybe the bullying in first gradewasn't the reason for what they considered "punishment" because as the manga goes on, any mention of the girl they bullied is mentioned less.
I think the real "punishment" or "karma" is their inactions in order to keep the status quo, so their mom is happy, so that their friends won't go away etc...
it's a form of denial that is very commen in young people, and it is turned up to eleven when you add gender identity
because of Akira's inactions, they acted and looked more boyish to apease their mom until Rumi's unknowing interference, their relationship with Rumi and Aoi (especially Rumi) became strained and hot/cold because they were lying about the truth, they agreed to go with Sunohara in a yukata just to make Emi happy, so when they turned him down, ONE could make the argument that it looked like they were leading him on (I don't agree with this argument), thus this caused to bridges burn between the three of them etc...
So when Akira FINALLY told Rumi and Aoi the truth, it was the their very first step to heal and grow into a person who actually expresses freely. it's going a long road, but at least she has a direction now with a great support system
Ps: they didn't sexual trauma from the porn video. the porn video caused ptsd caused the actress looked like them, and the position of the gang bang was similar to when they got assaulted when he was in first grade