The juror is there to determine the facts of the case. The prosecution and defense are both giving their sides. The jury may decide that there's reasonable doubt, doubt but it's not reasonable, or no doubt one way or another. It's their call. They really don't care about the agent's theories, because they are not FACTS.
I assume that the agent's theories were developed to support some set of facts that he had at hand and that those facts can still be pointed to in support of the previous theory. I've not studied this case in any detail, but I know that the goal of any prosecutor is to get a conviction, sometimes more so than being sure they have the right guilty party on trial. While in the ideal world, justice and truth might converge, in our world justice is on a clock and the truth is not.