Yes the DNA match is hard to explain - but there are many other reasons for thinking they got the wrong man - if there was ever a man to get!
No body was found - no gunshot residue on the back of the kombi where she says the attack took place, no footprints where she says "the man" looked for her with his dog, a pool of blood with no splatter or drag marks, Lees says she hid in the bush for five hours yet she was perfectly warm when found dressed in her shorts and sandals, she refused to speak to police or assist in any way, she emailed her lover within days of Falconios disappearance and many of Falconios belongings were missing from the kombi.
Suggest you start your reading with Keith Nobles excellent book on the case -"Find Falconio" You can download it for free.
If Murdock and Joanne were in such "intimate" contact that blood was transferred, the case is pretty well settled. The DNA evidence trumps everything else: random sightings by witnesses, inconsistencies in Joanne's recollection, and Murdock's adamant denials.
The claim that somehow Murdock somehow cut himself at the "Red Rooster" around 10:30 AM and around 3:30 PM, Joanne had contact with a drop of this blood and got it on her T-shrt is absurd. If the wait-staff there was so negligent that blood would not be cleaned during a 5 hour period, the blood would have dried completely and would not have transferred.
True, the Lab in Darwin was not "accredited"; whatever the legal ramifications of that may be, but even if the Scientist were completely incompetent and got the 16 out of 16 marker sites completely wrong, there would only be about 4 or 5 people in the WORLD who would fit that DNA profile. What are the odds that one of them fit the description of the perp, drove a vehicle that fit the description of the perp's vehicle, and was known to be in the vicinity when the crime occurred? One in Billions.
Without the DNA, the case would be pretty weak, I agree, but with it, the case is rock solid.
The real mystery is "where is Peter's body?" The only thing I can think of is that Murdock, realizing that he was in trouble after Joanne escaped, retrieved Peter's body and put it in his Pick-up (that's "yank-lish" for ute) and drove with it many KM's until he found a suitable spot in the desert to dump it.