Welcome back, Matt. I don't find you bitter or vindictive at all. There's such a thing as righteous anger--anger that is in its right place and appropriate. To have ever have been in a place where you have to wonder if a third party is going to gain legal rights over your children without your consent or even knowledge deserves anger. The things that have happened deserve anger. That you and your children are still coping with the fallout deserves anger.
That said, anger fades in time, if things continue to improve, as trust is regained, as you and your children recover from the damage that was done. Bitterness is when these events are long over and a person can't stop bringing it up again and again. I don't think that's what's happening here.
Your story, to me, illustrates the inherent flaws in polyamory. Yes, it seems to work for a few people. But as much as it's convenient to make Si the bad guy here, as much as she has done underhanded and sneaky, rotten things...she was expected to be content being forever on the outside looking in. I am not blaming you for that at all. I view you as the most blameless one in this whole story. I am not impressed with Si's behavior. I find it objectionable as you yourself do. Yet I also see a person who was expected to accept that she would be there equally for Ry, yet never have the benefits of a full time relationship with someone she was in love with. That's a lousy position to be in. She should have walked away and said no thank you, but that's hard to do when you're in love with someone and used to that person in your life.