It's interesting that Pegg decided to go with using the Yorktown here, given that ship's history as sort of a background precursor to the Enterprise-A. Could be a bit of foreshadowing to a possible replacement for the Enterprise after it gets torn apart and crashes (obviously renamed Enterprise).
What you need to keep in mind is that the Yorktown was going to be the name of the starship in Roddenberry's original 1964 proposal for Star Trek, before he changed it to Enterprise. The "precursor to the Enterprise-A" claim in the ST Encyclopedia is just an homage to that fact. So, no, I'd say "Starbase Yorktown" has nothing to do with the E-A. They're two parallel references to the same bit of Trek prehistory.
And they're very, very far from being the only such homages. There was a fan film George Takei did in the '80s called Yorktown II: A Time to Heal. (It was never released, but there's actually a team working on finishing it now, and there's a long-running thread about it in the Fan Films forum.) John Byrne's IDW Trek comics show the former Number One (from "The Cage") as the commander of the Yorktown. And so on.