It's probably been mentioned either way back in the thread or on Discord, but I'll clarify here to save people needing to search through many other comments
During the game, you can be in full-blown relationships with the bond mates, Leyala by default and the other two by choice. The Harem Members will be characters that are explored deeper, and you can grow closer too throughout the course of the game. The bonus encounters are mainly characters who you can have several sexual encounters with.
Atlas won't be an asshole by default to all of the girls. The only real exception to this was with
Gina when they are in America during Realm 1, and there was a logical reason for this, but by the end of that arc, he is softer with her. When we saw her again at the start of Realm 2, you have the choice to be harsh with her or to comfort her. How Atlas speaks to her after the encounter is also impacted by your relationship stats with her. He can come across as though she is just a hole to fill or that he actively enjoys his time with her. There will be story moments where some characters might act a little differently from how you would, but we aim for it to always make sense with the characters personalities/motivations.
As you progress through the game, your choices will impact relationships further and will determine how you treat other characters. But for the other harem members, you won't just be an asshole and treat them like shit just because. There will be a valid reason if that is the case, but most harem members will share a friendly and positive relationship with Atlas.