The foreign DNA was fragmented and degraded, whereas JonBenet's DNA was fresh and complete. The logical conclusion here is that the foreign DNA was not deposited at the same time as JonBenet's DNA, or both samples would be fresh and complete. It's not possible for one sample to degrade while the other doesn't - they'd either both be fresh and complete, or they'd both be fragmented and degraded.
The underwear JonBenet was found in were brand new and unwashed, straight out of the package.
Dr Henry Lee obtained a package of underwear identical to the one JonBenet was found in, day-of-the-week Bloomies, and when he tested them fresh and unwashed out of the package, he discovered they had DNA on them. Obviously this DNA was deposited on the underwear at the time of manufacture. If that happened with the underwear Dr Lee tested, it's logical that that's what happened with the underwear on JonBenet. In fact, I don't see another conclusion, given the differences in completeness of both samples.
Mary Lacy even said the DNA in this case may be artifact and completely unrelated to the murder. I really think the foreign DNA was already on the underwear when JonBenet was dressed in them.
Patsy's fibers were tied into the ligature knot, on the sticky side of the tape over JonBenet's mouth, and in the paint tray where the paintbrush used to construct the ligature came from. Patsy said she hadn't painted in that jacket, hadn't been near the paint tray in it, and hadn't been down in the basement in it. Transfer explains fibers on JonBenet, but falls short of explaining why Patsy's fibers would be trapped in the knot, tape and tray - unless that jacket was present when the paintbrush was obtained, when the tape was put on JB's face, and when the knot was tied.
When you compare these things to the amount of inconsistent stories and outright lies the Rs have been telling, and the complete lack of forensic evidence indicating anyone other than a Ramsey was in the house that night, RDI is a logical place to end up.