So sorry you are going through this. I am a retired social worker - had a career spanning some 30 years all in Children's Services (children up to 18) I also have a son (now in his 40s) from a previous relationship and when he was a teenager my DP (been together over 40 years) who was his SF used to pick on him for trivial things, and I always jumped to my son's defence, and that caused me and DP to argue. Mind it never went beyond DP getting annoyed at my son, and son arguing back. That was all many years ago and now they have an excellent relationship and have done for many years.
I think step-parenting and adolescence can be a tricky combination as is the case in your family at the moment. You say this has been going on for 2 years, which is a long time to live in this kind of turmoil, and I'm sure you are drained. Can I ask how you react when there is trouble between your partner and son. It's just that my DP told me (many years later) that it wasn't my son that annoyed him, but it was me always jumping to protect him, and so never taking DP's "side" as it were. Mind for me it was pure instinct to jump to defend my son. Actually I've just remembered my DP standing on the stairs and preventing my son from coming downstairs but he soon gave way. I honestly don't remember how long this went on for, but a couple of years I would say.
As far as social services is concerned, I am surprised they are involved tbh given that your son is 16 because although still a minor legally, they do tend to be less proactive with 16 year olds. If they went down the safeguarding route they could go to court to ask for a Care Order if they believe they had grounds. This would mean they would have parental responsibility (PR) You wouldn't lose PR but the LA would be in the "driving seat" so to speak. BUT I think it would be extremely unlikely for them to seek a Care Order on a 16 year old. If they did and were granted one, they would place him in a Children's Home or with foster carers.
Where is DP spending 5 days a week? This isn't really a workable solution is it - ok it might satisfy social workers that your son is not going to be harmed by his SF, but it could possibly cause even more resentment/tension between your son and partner couldn't it? Have social services attempted to sit down with you and help your partner and son to have a better understanding of each other, and avoid these confrontations. Adolescence is a time of great hormonal imbalance and this can cause aggression, especially in boys because of the testosterone. I think SFs can see their authority being challenged and can't cope with that and this can lead to trouble. I think this can happen in non step families too - I worked a lot with adolescents and family conflict. This might sound strange, but this sort of behaviour between the adolescent and the male can be seen in apes, especially baboons, as the adolescent males try to "flex their muscles" and the dominant male reacts.
Hmm.........where to go from here. Can you and your DP communicate about what's going on. Is he willing to recognise that he needs to stand back and avoid confrontation with your son? Are you happy in the relationship (apart from the problem obviously) is he a good father to the younger children.
You need family therapy really, so that everyone in the family can have space to talk about their own feelings, and a trained therapist to encourage this expression and work on conflict resolution. I don't think the LA will be up for paying for that though!