I think it's a bit or a reach to say that the statement leaves room to claim that they do have Nazi links/associations.
He said:
I have never believed or intended to assert that Kellie-Jay Keen and Angela Jones are Neo-Nazis. It is also now clear from public statements made by Ms Keen and Ms Jones that they share my belief that Nazism is odious and contemptible.
Why would they have links with groups whose beliefs they consider "odious and contemptible"? It doesn't really make sense.
I think your reading of his statement is being coloured by your own view that KJK has links/associations with the far right or Nazis, evidence of your belief being some of the MN threads which you refer to and which were started by you.
But in his apology he was allowed to express criticism for people "knowingly sharing a platform with or associating with individuals who hold or express these extremists views" and that suggests to me it wasn't clear cut no associations/links existed.
I don't see how you can draw that conclusion. In the first place, the whole point is that she did not "knowingly share a platform" with the Nazis in this incident. They turned up uninvited and unwanted. (And unchallenged by the police or by the supposedly Antifa crowd.)
But more importantly, his remark simply means that he and perhaps you have a different idea of what free speech means compared to some other people. "Links" would have to be substantive, not just sharing a platform, whatever that means.
There is always a risk of an adverse judgement when you go to court, however strong your case. Not to mention the eye-watering expense. So KJK may have decided on that basis to take the offer of a settlement.
They may have compromised on the exact wording, KJK may have agreed not to lay into Pesutto in public, or on her channel.
But on the meat of the case, the point at issue - that Angie Jones and KJK were Nazis or Nazi sympathisers - the statement is an unequivocal retraction and apology.