Mr. James Winters has finally offered his take on Phonemic diversity supports a serial founder effect model of language expansion from Africa. The Return of the Phoneme Inventories:
There are several assumptions made in the paper that I’ve already considered investigating in my own work. Most notable of these assumptions is that the serial founder effect model is the only explanation available. As in population genetics, where numerous papers have supposedly verified the out of Africa model, Atkinson doesn’t really test any other competing hypotheses. It therefore makes it hard for me to accept he’s really shown that geographic distance from Africa is concomitant with a series of population bottlenecks for phoneme inventories. Indeed, with bolstered support for Neanderthal admixture in some human populations, it is becoming increasingly likely that the serial founder effect model is unlikely to hold true in relation to genetic diversity... ... I’m not saying that Atkinson thinks that serial founder effects are solely responsible for the observed patterning (as noted in the quote above)… But I do think the model’s flawed on several theoretical grounds. Specifically, Atkinson hasn’t ruled out the possibility of selection as having shaped these languages according to different socio-cultural niches.
Again, I can't speak to the linguistics.
But overall I believe that cultural evolution has more freedom in terms of the dynamics of transmission, and so is less likely to be captured by an exceedingly general model.
In other words I think the space of possibilities of plausible models for the patterns we see in population genetics is smaller than the space of possibilities of plausible models for the patterns we see in linguistic diversity, mostly because the transmission of culture is much more plastic, flexible, and rapid in action.