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Well, Atkinson has made his claims of a serial founder effect before, and linguists have been less than impressed (See Mark Liberman's response here and two anthropologists' response here). In brief, linguists have taken Atkinson to task for assuming that Southern African phoneme inventories are preserved features rather than innovations; for neglecting things like vowel length and syllable structure (and a bunch of other relevant features, showing his unfamiliarity with the field); for an unworkable approach to tonal features; and for generally ignoring things like areal influences altogether.
The current consensus is that the origin of human language a) is so far back in time, b) originated in different (and non-extant) species to us; c) lacks clear evidence (or even reasonably indirect evidence); this means that no-one can know much about it (for the time being). Inferring or even claiming such definite knowledge about the origin of language from their present-day distribution as Atkinson does is beyond all reason. Perhaps even sensationalist and dishonest.
The major contribution of these sorts of articles, and by implication with arguments such as this one by Atkinson, is that it articulates a position and then allows us to critique it. I don't get the impression Atkinson meant his claim of an Ur-language as a thought experiment, but it's useful as this, if nothing else, especially to the layperson.