The way Kiibo responds to this is interesting to me because this is Kokichi, who’s putting on his childish facade. What he said reads more like a 'shit-talk’ than it does a sincere comment, and Kiibo’s picking up on that much. But at this point, whether he realises or not, he knows when Kokichi is trying to provoke a response out of him, if not entirely the reason for doing so.
Which is why Kiibo’s so nervous- he’s not even so much angered by Kokichi’s ‘flippant comment’, he’s worried. The disconnect between his logic and his ‘hope’ is starting to show in cracks, and he doesn’t have any basis for his belief.
What’s more, Kiibo is learning to doubt more than believe. If his commentary in the Virtual World, his questioning of Miu throughout this and Chapter 5, and when he suggests to seriously consider if Gonta was capable of murder is anything to go by, he’s not nearly as sure of things, or people, as he sounds. So when he talks of ‘certainty’, that must be the ‘inner voice’ talking, because Kiibo himself sure as fuck doesn’t look certain.
But what’s fucking him over, is he isn’t allowed to voice that thought, even to himself.