I'll take a stab at this.
As you correctly point out, the evidence can't be reconciled. Normally you could just discount the ARCCA experts as hired guns, but because we know they were instructed by the Feds, we can't do that here.
This irreconcilable knot shows that something is wrong in the evidence/theories. The defence allege this is due the defendant being framed. That's one theory.
Alternatively I think the state just did not put together a cohesive reconstruction - which might partly be because the lack of clear data from the vehicle. But also incompetent analysis.
For instance, I am not sure how hard the Lexus really would have needed to strike him in order for him to fall and break his skull. I've seen other cases where someone was knocked unconscious in a fight, fell on a hard surface and was fatally injured from that fall. Which is actually what the defence allege.
Not being a reconstruction expert - i have no idea about these things. For instance is it possible John staggered, then fell where he was found? Or other way around? But obviously if the CW cannot come up with a credible reconstruction, the verdict must be NG.
I tend to agree that the CW theory as presented was internally inconsistent - but that could be simply due to incompetence as opposed to framing. IMO.