Sometimes I wonder if maybe he's just doing you a huge favor. Do his values ever align with yours? Kids are resilient and come not fully formed. Some of the things you fret about are things Sophie has time to decide about herself.

If you spent a lot of time explaining polyamory to her and the relationship between the three of them doesn't have longevity then what.

Expose her to the variety only if you want to or say he turns over a new leaf (don't hold your breath!), wait for her to ask questions and then be honest. I think it's fabulous to be non judgmental unless you really don't have a strong opinion. You can always explain that there are things she doesn't need to worry about because she is a kid and some things are grown-up things or you can tell her 'well I don't like that but that doesn't mean you can't" and then have a discussion about what she thinks. Don't be surprised if she tends to favor your ideas and feelings. That is what gives her comfort...feeling kinship with her most beloved person.

In the not too distant future your ex might have to face Sophie's feelings (or lack thererof) for him. She probably won't get too upset about it because you haven't harped about him to her. You're protecting her from the shit pile that he shovels away from himself. Nobody said just because of your history with him that you have to take on his shit pile.

Half siblings, step sibs might be too confusing for her to even think about if she has no contact with them. She sees and hears about other kinds of families at school. She will make up her mind about what makes a true family in her own time but you are the one who will make the standard. I would celebrate it...as in well this is our family and this is how we roll.