Headcannon: Dazai only really knows how to deliver results and that's why he is confused at Atsushi's assumptions of him.
For starters, Dazai is not a heartless person. While he claims that evil and good don't sway him, I don't think that's the entire truth. People do sway him, regardless on if they are good or not. Dazai genuinely loves or at least cares for them, but does not express it normally.
Chuuya wanted somewhere to belong and to believe he was human. Though he never asks these things of Dazai, it doesn't stop Dazai from delivering them. He all but drags Chuuya into the mafia and places him in a partnership so devastating that they're still going on missions as that duo while being enemies. He is shameless in his compliments to Chuuya. Though he irritates Chuuya, it's all done with a precision that shows that Dazai pays attention and cares about him. It won't save Chuuya from pain, but Dazai would never allow Chuuya to die if he could stop it.
Kunikda has extremely frigid ideals. Dazai challenges this constantly because he is aware that the world is not so idealistic. Even in the smallest ways, such as disrupting his schedule, he is challenging Kunikida to grow. Their partnership is to an extent sweeter than Chuuya, but does involve some soft occassional interference disguised as being a nuisance.
It even goes to Akutagawa. While the way he treats Aku is not okay, he does not hate him. I'd argue that Dazai actually really likes Aku. He speaks highly of his power to Oda, spares his life despite his insubordination (as they are in the mafia, Dazai could have easily killed him for disrupting an important mission), and views him as worthy enough to be part of the next Soukoku. However, his way of driving Aku into his full potential is through forcing Aku to view him as a superior who's acknowledgement is worth more than his life. Dazai fills the gaps left behind with violence. He is absolutely capable of being tender with Aku, he just thinks that it would devalue his authority to Aku and so maintains a cold demeanor even to this day. Even as Aku has come to hate him, he still idolizes Dazai. It won't matter to Dazai because he delivered in his promise to give Aku a purpose. He has successfully made Aku stronger by introducing Atsushi into his life.
In any relationship Dazai has with people, he is achieving something whether they have asked him to or not. He doesn't seem to care about their perception all that much. If he is seen as lazy, abusive, terrifying, it's all the same to him. Still, Atsushi surprises him because his assumptions of him are not negative. By all accounts, he is as manipulative to Atsushi as he is with any member of the agency. He is as roundabout with him and even has a moment of cruelty that mirrors his time with Aku. He has heard about who Dazai was and has seen who he is at the moment. With all of that information, he seems to be the only one who has vocalized to Dazai that he views him as a good person.
Dazai knows he gets results. He knows he is valuable by every metric. He knows his partners rely on him and are willing to put their life in his hands because it's safe in his hands. Dazai knows he can be evil, that he can be cunning enough to be labeled the Demon Prodigy. Though he has been trying for a few years to go about things in a way that may be closer to what his departed friend would, it never occurred to him that he could be considered a good person. He only knows he can make "good" things happen for those around him. Hopefully this makes sense.