Let's talk about Lucy's advances towards Augustus in "Burnt Bridges" because it was bad and honestly had the potential to be so, so, much worse.
The color is all pink like this might be a romantic moment. Let's call this scene what it is: it's Lucy assaulting Augustus. She does not telegraph her intention to kiss him, giving him an opportunity to turn her down. She just goes straight for the kiss.
Augustus has to physically push her off and tell her "No".
Even then, once he's pushed her away, expressly told her "No", and is clearly upset, she tries to go for another kiss anyways.
We also should acknowledge that is happening his bedroom, which is the first place he's had to himself that felt safe. If we consider the layout of the room, Lucy is physically between him and the door. It's a windowless basement room with no other exits. To leave, he has to go around/through her. He can't easily just walk away.
It's only after he threatens to make a scene that her family will hear and invokes Lucy's rhetoric about consent that she actually stops.
While clearly upset in the moment, overall Augustus doesn't seem to be very affected by the assault. He comforts Lucy through a self-loathing spiral, accepts her apology, and affirms his platonic love for her. There is no indication that he feels less comfortable around her going forward; if anything, her breakdown drives him to be more protective of her.
And I genuinely think what we got in canon was just about the best possible way for this to play out, because the alternatives are so much worse.
In canon, Augustus's sense of safety wasn't damaged, but given the situation, it very well could have been. Lucy came into the one place he should have unequivocally felt safe and assaulted him. At this point in the story, he hadn't really started making friends with Jordan and the seniors; she is his only friend. He's living under her roof and doesn't have anywhere else to turn. He would have no one to even talk to about this, even without the stigma surrounding it and the worry if anyone would believe him or take him seriously.
And if Augustus was really uncomfortable with Lucy, it would have really messed up Lucy too. In canon, she immediately spirals into self-loathing for what she did and Augustus helps comfort her through it.
A version of events where Augustus removed himself from the room because he was uncomfortable and would have reaffirmed Lucy's perception of herself as "a bad person" and left this self-loathing spiral completely unchecked. In the aftermath, she wouldn't be able to turn to Augustus for social support anymore.
It's also worth acknowledging how Lucy is putting him in an incredibly bad position in relation to his housing. The only rule we actually see Lucy's parents establish was him not having a romantic relationship with Lucy:
If he were to reciprocate, he would be risking his housing, and being kicked out of her home would land him in a worse scenario than he was in before he left. At best Toby and Alejandro are angry about his lack of loyalty and at worst Alejandro has been told about his relationship with Melanie and is homicidally enraged. Augustus has been afraid of Alejandro's wrath to the point that he gets held back a year trying to appease Toby. His options would be to go home expecting to be severely beaten or to immediately become homeless.
It's also worth noting that Lucy has positioned herself as having control over Augustus's housing as well. She's the one who persuades her parents to take him in. She also lays down conditions for him staying there:
How would Lucy's parents know if Augustus was skipping class or pursuing Daisy? If Lucy told them. She never threatens to have him kicked out or tries to leverage his housing against him, but him remaining in Lucy's home is implicitly contingent on him having Lucy's support. She has a lot of power in their relationship, and just because she doesn't wield it against him doesn't mean Augustus isn't aware of it.
Augustus has a lot to lose if his relationship with Lucy sours. There is a parallel between Melanie and Lucy in that they're at the time of their advances, they're the only real friend Augustus has. We saw Augustus passively acquiesce to sexual advances he wasn't really ready for with Melanie.
Fortunately, when Lucy makes advances, Augustus is older, more willing to assert himself, and knows more about consent from his conversations with Lucy. Honestly, Augustus shows a lot of trust in "Burnt Bridges". He trusts that Lucy doesn't want to hurt him or take advantage of him and he trusts that if he had to make a commotion and involve her family that it wouldn't backfire on him.
Augustus is really at his best in this scene; he clearly deeply cares about Lucy and it reflects well on him. I'm glad that he was resilient enough not to be really aversely affected, but I think it would be completely understandable if he was.
It's always been wild to me that this scene doesn't often come up in conversations about assault in the comic. Honestly I think there's a big gender bias at play and suspect if you swapped the genders of Augustus and Lucy people would have reacted very differently to this scene.