No offence meant .. but I interpret your first sentence as being at odds with the rest of the paragraph.
What I'm getting at is that, officially, he was seen (but not necessarily witnessed) doing this, which diminishes (but doesn't entirely undermine) the plausibility of what you are driving at. However, without knowing more about the case, I can't say to what extent witness evidence was considered probative.
By the way, it's a paradox to say this, but it's also true that just because witness evidence is inherently unreliable in the sense of a wont of accuracy, it needn't follow that it is lacking in credibility. If I say, 'Yes, that's the man', I may not be able to remember if he had a beard or green eyes or whatever, but I may still pick him out.
There can only be two answers: either nobody present knew Mair; or he couldn't be recognised, on account of not being involved in the incident.
There's a third and a fourth possibility:
(iii). He was recognised by a witness who knew him and thus he was positively-identified as the assailant.
(iv). He was followed by a witness who did or did not know him, and thus he was positively-identified as the assailant.
It's a bit late for that isn't it? Have you seen the footage and court portraits? Something has gone very awry here.
Are you certain you have seen all four episodes? The would account for approximately 3 hours viewing.
I see a flaw in your reasoning here, which is that you are starting from the tendentious assumption that it wasn't him in the dock.
Let's consider three further facts:
1. As he attacked poor Jo Cox, the assailant shouted, "Freedom for Britain, Death to Traitors."
2. At his first appearance before Dewsbury Magistrates (I think it was Dewsbury, I'm going from memory), when asked to confirm his name, the man stood in the dock said or shouted: "Freedom for Britain, Death to Traitors".
3. A man known as Thomas Alexander Mair has not been seen in Birstall since 16th. June 2016. He was - apparently - a socially withdrawn man in some respects, but he wasn't a hermit. Lots of people knew him and he had friends, family and acquaintances.
Points 1 and 2 tell me there is a link between the man in the dock and the tragic killing of Jo Cox. Not that it proves anything, but it tells me that the man arraigned was the man suspected of the killing.
Point 3 tells me that Thomas Mair has gone somewhere. Where has he gone? On holiday?