Im sorry but that 16 year old kid was way too dumb to make up any of that stuff he told the investigators, leading me to believe that what he told them about raping and killing her likely happened. The conversation he has with his mother is pretty damning. Also they left a lot of evidence out of the documentary. The defense attorneys were doing their job, trying to introduce doubt in the jury's mind. I very highly doubt that Avery was framed; he's a violent felon (the incident with his cousin, the cat) and seems very capable of the crime. I also doubt the FBI would willingly go along with the Sheriff's department. The amount of corroboration that it would have taken to frame Avery is just highly unlikely.
I really think that they killed her somewhere else outside explaining the lack of dna evidence in the trailer.
With regards to the FBI are you talking about the EDTA test? If so what was testified to went with a range that hasn't been established as solid evidence that it was in the sample or not.