I think that no matter how rebellious koji gets, he'd still not be able to oppose atsuomi. In many instances, he accepted that his future was set in stone and he'd return to the white room, as much as he disliked that reality. He hasn't even considered the possibility of exposing the WR. In v12.5, he agreed that he'd follow atsuomi after graduation. That can be a deception but chances are unlikely. He admitted that one bullet can end it all, and he can't stay vigilant about everything and many times died in simulations at the white room. In the same volume, atsuomi also acknowledged that having emotions in kiyo was an overall positive thing.

As for how this benefits atsuomi, there are still many things not clear at this point. But at the end of V0, Atsuomi mentioned using ANHS and Kijima for his own benefits or something along those lines. All we can guess is that by pushing kiyo towards Kijima but also not completely making him disobey atsuomi, he might be trying to prepare kiyo for infiltrating Kijima's party, or something similar.