Interesting, septimus! I looked at the cited Nature paper, and the first thing that struck me was that according to that reconstruction, the approximate date of the divergence of “the Italic, Celtic, Balto-Slavic and perhaps Indo-Iranian” language groups is pretty nearly the same as the date estimated by the more mainstream model.
That is, everybody seems to pretty much agree that those language families emerged and began diversifying within about the last 5000 years: i.e., later than about 3000 BCE (they propose Greco-Armenian languages becoming distinct perhaps two millennia previously).
In other words, this model’s dating of the language evolution process involved seems less radically divergent from the more mainstream view than you suggest.
AFAICT, where the one major difference of opinion comes in (and it’s admittedly a huge difference) is in identifying the approximate date where the breakup of Proto-IE into separate language families starts. The “mainstream” view holds that PIE began branching only around 5000 BCE (plus or minus some centuries), while the Nature authors’ model pushes it back to around 7000 BCE, with Hittite, Tocharian and Greco-Armenian diverging early.
If some “literacy effect” had caused the authors’ fundamental assumptions about the intrinsic speed of vocabulary change to be incorrect by some constant “stretch factor”, I would have expected their conclusions to differ from the mainstream model consistently across the board. Wouldn’t you?
That is, wouldn’t we expect a “vocabulary change clock running too slow” to give inflated estimates for all the time periods of linguistic change that it covers? Shouldn’t we see, say, the emergence of Indo-Iranian, and then its split into Iranian and Indo-Aryan, etc., pushed back in time as well, when compared to the mainstream model?
But that’s not what the paper appears to show. So I think we can infer that whatever the merits or faults of this linguistic evolution reconstruction model, the problem, if there is one, is not as simple as just using a too-slow base rate for vocabulary change.