How do we know that all time travel instances that started after 2233 and ended before 2233 still happened in the new timeline, though?
Because, as of the point of divergence in 2233,
both timelines are possible futures.
Remember, ST09 didn't
erase the prime timeline, so any travellers coming from a point after 2233 (in EITHER timeline) can travel back to a point before it. And even meet each other - because before 2233, there is only one.
It's exactly like a road which diverges into two 'forks'. Travellers on either branch can walk or drive backwards along it, until they reach a point before it diverges. Then they can both interact. Same story here.
As for Pegg's comments? The hell with it. I hate to sound dense, but he can say whatever he likes - doesn't make it true,
until a film proves it. And until that time, Pegg's theory is just that - it's only a theory.
And the so-called "inconsistencies"? Let's run with that:
- Pike's age? You know, I wasn't aware Bruce Greenwood was the only recasting of a role we've ever seen. Gee, how COULD I have missed that?

(seriously, we have no idea how old Pike actually is - in EITHER timeline - and recasting of roles is so absolutely widespread that this doesn't mean anything. You don't see people whining about alternate timelines just because James Cromwell looks older than Glenn Corbett, do ya?)
- Earth's cities being built up: Again, we almost never SEE Earth in the prime timeline, so the depiction of San Francisco is hardly a problem. And even so, by the time we see Kelvinverse SF, 30 years have gone by since the timeline divergence. They can do a lot of building in that short a span.
- The
Kelvin's size: Who's to say Starfleet doesn't have a wide range of ship sizes? They can have big ones, small ones, the whole shebang.
- Khan's genocide, or lack thereof: I've already said how much I believe the horseshit about there being no massacres under Khan's rule. I just chalk that up to Augment propaganda. Khan, even as portrayed in TOS, is exactly the kind of person who WOULD commit massacres (just ask the crew of Regula 1) and the only reason anybody ever said there weren't any massacres is because his dictatorial regime didn't allow anyone to know about them. Augment rulers could hardly NOT massacre, anyway - it's what they were literally made to do. The concept of a benevolent Augment is a contradiction in terms, if there ever was one.