OP, you have moved towards the right position I think in acknowledging that it is great your DS has people in his life who care for him and he likes. That is so so much better than him feeling unwelcome or deprioritised in his home with his dad etc. you will have these disruptions, however well things are managed, because it is a bloody complex, emotional thing you are all managing.
However, the key is to pull yourself back from spiralling into conflict. Assert your boundaries, yes. But don’t start dismissing another woman, who cares for and is doing a ton for your child, as batshit or crazy. I do agree if she is trying to control how your son is with you, that is very unhealthy. But there could be different interpretations… eg when you are all together, she may just be anxious to display to you the closeness she has with your son, so you know she is being a good step mother. That could come across as intrusive or competitive, and would be immature on her part, but pretty understandable.
I do sense your son may also be feeling from you that it will upset you if he is a certain way with the step mum too. The discomfort he has on the phone could in part be because he knew you were around watching him. Or some of his worry about the gift originally be thinking it would hurt your feelings. Do check yourself with the boundaries you are setting. How much is for the welfare and happiness of your child? And how much for your own ego/ because sharing your child with another woman is intrinsically painful?
I ask all this with full sympathy. My ex left me when my DD was 6 for a woman fifteen years my junior, with whom he was having an affair. That woman has become DD’s step mother for the last ten years. I have never told DD about the cheating. DD had quite a crush on her at first, and would come back to me and tell me this woman was better than me because she was younger and funnier and did cartwheels with her. I told her I was glad she had someone fun and young to play with. DD asked me to do her hair before going to her dad’s because she wanted to look pretty for this lovely, fun woman. Sure thing I said. Every year, I create a photo book for DD, and I include photos of this woman and that side of the family. Every year, they come for birthday celebrations at my house. And on Mother’s Day, I gently encourage DD to remember to thank this woman, if she wants to. I say “I know she’s not your mum, that is my joy and privilege. but today is a good chance to thank any woman in your life who cares for you and does motherly things with you”. Is it hard for me? Fuck yes. But the reality is, despite how this woman came into our lives, she is an excellent step mother. She cares for DD and she does a lot for her. Dad isn’t useless but is a typical entitled male. I know for a fact when DD had nits, it was this woman on her knees at the bathtub, shampooing and combing them out. And she now has her own children, and is continuing to integrate DD into that family with sensitivity and care overall. That said, there are upsets. And sometimes I get fierce, in private, on behalf of my child. But actually these upsets tend to be me fighting for her full inclusion into that family, not the opposite.
Anyway, it’s very complex, and it sounds like you are doing great overall. But I do encourage you to continue to work collaboratively, with an appreciation for the complexity on all sides, versus turning it into mudslinging and getting more militant. In the end DC are far better off with a ton of love and parental presence, and it is rare this feels traumatic for them unless they are torn within a power play between adults.