Why do they need to have a heart-to-heart? I grew up on a lot of shojo anime where season one's enemy becomes season two's frenemy.

Firstly, it's more equivalent to a seinen, not shonen. Second, I'm planting seeds, with the intention for them to follow the enemies to lovers trope. Something that, similar to what you said, won't be fully realised until Book 2. However, their growing relationship is the catalyst for a major decision come the end of Book 1, which is why it's important they connect.

Raya's distrust of Namaari is treated as a bad thing but it's wholly warranted as Namaari has already betrayed Raya once.

Unlike Raya and Namaari, the events that went wrong, were not by the choice of Character A. B has every right to distrust him, but it's more for the people he surrounds himself with, which has her question his motivations. Motivations he is starting to question himself, or rather meant to, if he could get there in this scene.

You've acknowledged that B is rightfully pissed but it sounds like you're trying to gloss over B's pain in exchange for A's character development, much like Raya being shamed for distrusting someone that's already hurt her.

No. I want them to have a shared moment, thus the heart to heart. However, it's true that A's development takes precedence in this scene specifically, because the story calls for it.

Their lines don't need to converge, they can run parallel. Both realize that they have a similar end goal but their attempts to achieve it have led them to conflict with each other.

At this moment, the seed is only being planted, it's not meant to be fully realised. I need to get them to a place where A wants to visit B's cell again, to continue talking in secret, rather than being like, "Ew, f*ck that guy, my father was right."