That timeline theory Pegg relates in that link (which actually originated with the revised
Star Trek Encyclopedia by the Okudas, though Pegg apparently got a look at an advance copy) isn't meant to say "none of this happened in Prime." It's just meant as a patch for any minor continuity glitches hard to reconcile otherwise (like, say, the oddly built-up Earth cities in Kelvin compared to Prime), or as a license for future filmmakers to take more liberties if they find it useful to do so. (Although the irony is that the movie Pegg wrote,
Beyond, had much less need for this license than the first two movies did, because it meshed more smoothly with Prime continuity.)
After all, these are ultimately just stories. "Canon" doesn't represent anything real or binding (just ask Bobby Ewing on
Dallas); it's just a shorthand for the way the creators of a fictional property decide to depict their reality at any given time. And whether the people telling a story choose to reference something from a related story is usually a matter of popularity. Something that's part of the same continuity but widely hated will generally be ignored or quietly erased from canon (e.g.
Voyager: "Threshold"), while something that's a popular part of a different continuity can be added to the main continuity (e.g. Harley Quinn, Agent Coulson, etc.). So whether the
Kelvin and ships like it end up in Prime isn't a matter of timeline physics or what-have-you, it's a matter of whether future storytellers like the idea enough to integrate it. And the
Kelvin and Captain Robau were pretty popular elements from the 2009 movie.
The main thing that might get in the way of crossover elements is that the movies are produced by Paramount and Bad Robot. CBS owns all of
Star Trek, but Paramount and BR have a stake in the elements created for their movies, so a CBS production like
Discovery might need to shell out a little more money if its makers wanted to use a concept from the Kelvin films.