mtDNA really does mislead people! Completely different species can have 100% identical mtDNA. mtDNA has virtually no affect on traits like colour, pattern, size, scalation, ability to breed with other individuals, food preference, or anything else we'd recognise as 'traits'. It tells a bit of the story about the history of population separation, but that doesn't always have anything to do with speciation or local population differentiation.
The DNA which makes one snake large or black or spotted or striped or like to eat birds or have large teeth or heat pits or climb or burrow or have big belly scales to slither on land or keeled scales to stick in rock crevices etc. etc. is all nuclear DNA, not mtDNA. mtDNA isn't even in the nucleus (where the 'real' DNA is).
As far as the morphology etc. of species goes, mtDNA says nothing. The mtDNA shows that Carpet Pythons along the east coast freely interbreed and have probably never been separated, but that doesn't mean they can't differentiate (which they obviously have). It also shows that the term 'intergrade' is probably not correct to use for these snakes, because it is not a case of two different things which evolved separately coming together and making some hybrids while others remain pure, it says that they were probably all once the same and are slowly becoming more different along the span of their distribution - it's the opposite of what the 'intergrade' concept suggests is going on with these snakes.
With mammals the biological species concept (if animals can breed together and make fertile offspring they're the same species) works quite nicely, but in snakes it doesn't work at all; according to it *ALL* pythons are the same species. Reptiles have really weird and robust DNA, so the genetics rules don't really work with them. It's obvious that there are big genetic differences between Diamonds from Sydney and Carpets from Townsville, so the mtDNA being identical is clearly misleading. Because of the continuous gene flow and the probable recent divergence in traits between these areas there is probably a fairly small *number* of genetic differences between, say, Carpets from Sydney (or Gosford or wherever) and Carpets from Brisbane (or Townsville or Cairns or Prosperpine etc.), but they are clearly very big and important genetic differences. You can get two different species which are virtually identical to look at and in their way of life, but they can have a huge number of genetic differences. Or, you can have just one single nucleotide of difference (the smallest possible genetic difference) and have the difference between a black snake and a white snake, or a speckled Lace Monitor and a Bell's phase, or a large animal and a small one. Get, say, 20 of these sorts of 'big impact, small genetic size' mutations and you have a radically different animal, but that difference is almost impossible to detect with normal DNA analysis.
The geneticists don't like to acknowledge this because it makes justifying their claims more difficult, and would often invalidate the claims they want to make. Unfortunately, it leaves a lot of people misunderstanding what's going on.