I don't have time to follow the math through in detail so I can't be certain, but I believe there is no simple way to extract the age estimates. The problem is that the mutation rates in mtDNA vary a lot from site to site. At the average mutation rate, you don't have to worry much about the same site mutating multiple times over a few million years, but in reality, with the rate varying so much, some sites will mutate repeatedly. Therefore the divergence between the mtDNA of two species does not increase linearly with time; instead, it increases more and more slowly as mutation saturates the more mutable sites.
If I have understood the background papers correctly from skimming through them, they're modeling the distribution in mutation rates as a gamma distribution with a shape parameter of 0.11. This is a highly skewed distribution, with high probability of low values and a long tail of high values. I.e. most mtDNA sites mutate pretty slowly, but there is a wide spread of mutation rates out to very high values. This is certainly consistent with what I know about mtDNA mutation rates. So you really have to use a fairly sophisticated model to extract an age estimate under these conditions.
(There's another effect you have to worry about here too, which makes it wrong to simply take the ratio of Neandertal/human divergence to human/human divergence. The problem is that population ancestral to humans and Neandertals had some mtDNA variation in it (comparable to the levels seen in modern humans, perhaps), and some of this variants went into the Neandertal line and some into the modern human line. To correct for this you have to know the effective population size of the ancestral population, but I don't think this is a large contributor to the problem here.)
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