Beyond that, I also wouldn't say they made it out as if Avery was clearly innocent of the murder of Halbach. What they did make clear was the absurdity of the investigation and the trial, but that isn't the same thing.
I understand why people are hung up on trying to figure out if Avery actually did do it, but the main point of the documentary to me is how law enforcement perverted justice to send Avery and Dassey to prison for a very long time.
With Dassey in particular, if someone included his confessions in a fictional story people would be incredulous. Yet in reality, the investigators blatantly fed him what they wanted to hear, his attorney happily went along with it, the prosecution had no qualms about using the information in court, the judge didn't toss out the confessions, and the jury went along with the pieces they did hear.
Ultimately, this is a story about getting crushed by the machine. If the machine wants you to go away, you are going away.