Rather, the Okudas' revised Star Trek Encyclopedia suggested that Nero's arrival caused ripples back in time that might have created a slightly new sequence of events before Nero, thereby explaining away any minor inconsistencies between the Prime and Kelvin universes (e.g. perhaps the much more built-up San Francisco in Kelvin, or the disproportionately large Kelvin itself). Simon Pegg alluded to this a month or two before the STE passage was released to the public, presumably because he'd gotten an advance look at the text, and that created the misapprehension that it originated with him, due to people's unfamiliarity with how long the publishing process takes (especially for a book as complicated as the STE). But, ironically, Beyond itself meshed more smoothly with Prime continuity than the prior films did, and actually had less need of such a handwave.
Either way, the intention of the passage was never that the revised timeline would be "entirely new" -- I mean, obviously both versions still have Kirk, Spock, McCoy, the Enterprise, the Federation, etc. It was just a way to justify any continuity issues that might arise. It certainly was not meant to compel discontinuity.