I haven't read the plot in a while so it might not be the most accurate but basically, Brett and Hayden were never really together from the start as a romantic couple, they both just loved having sex with each other, but then Hayden falls for Brett and saves his life in a bad incident that happens at a frat party (end of season 1) then through season 2 Hayden comes to head with his feelings for Brett and even confesses but Brett (who's more than likely some type of sociopath) never really reciprocates romantically to Hayden's advances, though he is obviously starting to get attached to him. At one point because of plot, Brett gets into a car accident that was orchestrated as an attack against him and then sth terrible to him. Brett does not exactly react the way you'd expect someone that's well adjusted to react and instead hides it from Hayden and weaponises it to win agaiinst the man who orchestrated the attack on him, which leads Hayden to be hurt by it and they have an argument and "break up". that's basically how season 2 ends. Theres a time skip now for season 3 which seems to be around 2-3 years maybe.
You hit the nail on the head, it ties with both of those things and Brett's experience with his older brother (who's a beta and i think was sickly as a child). Brett had noticed his brother was into these tiny glass statues in the shape of a bird and when he went hunting with his dad he brought the dead bird to his brother to cheer him up, his brother freaked out and looked at him like he was a monster/weirdo. The same expression Hayden bears after Brett explains his logic for lying/hiding the terrible thing that happened to him so Brett probably as a way to protect his own growing feelings and in his mind being "rational" decides to end things with Hayden and then yeah two years jump but as we can see in the final chapter uploaded here Brett is bothereeed as fuck lmao

What was the main conflict? Why did they break it off again, and were they even ever dating or just one sided?
Hayden is the top, Brett is the bottom, right?
I saw some spoilers below. I would love more, I just don’t have time to go through it all.
What’s going on so far in the raws? Someone said the top tries to distance himself but it’s comedic and doesn’t work out?
If the bottom distanced himself from the top, how come in chapter 47 or new chapter of season 3, they reunite? The part where the top goes up to the bottom who is wearing a red scarf.
Where was the bottom all this time and why?