I think Siwoo's alpha wants to dominate Byul's alpha, but yk alphas are not used to be the submissive type in relationships so hence Byul's reaction. Maybe he's startled by the sudden domination, and like he said it was his first time feeling Siwoo's pheromones. I forgot whether Byul was recessive type or dominant type, so I can't go further with my understanding.
Also, I think Siwoo believes that Byul decided too soon about his feelings towards Siwoo... that's maybe why Siwoo had to sprinkle some reality into Byul's head. A simple reality check of what's gonna become of their future, basically foreshadowing issues they might face as both alpha in a relationship. Siwoo's being pessimistic because of the future that's yet to come. He is over thinking.
This is actually such a great view and explanation because let’s be fr Byul is unrealistic and lives in Lala land, and Shiwoo knows that so like you said it makes sense he wanted to really make him think about his feelings instead of “oh i liked the physical contact with you, but not them” his feelings aren’t really based on shiwoo as a person but the sudden kiss they had and shiwoo wanted to make sure he understood his feeling before he allowed Byul to confuse both himself and shiwoo even further, even if it hurt shiwoo not to indulge his emotions.

Ok so two alphas releasing phermones cause aggression(?) because they both want to be dominant BUUUUUT why wasn’t this the case when Siwoo broke up the fight between Byul and that other guy?? WHATS GOING ONNNN