What about the different design for the cryogenic capsules in Into Darkness? How do we explain that?
Was it ever actually stated that the capsules seen in the film were the same ones from the Botany Bay
, as opposed to newer ones they were moved to?
If that was stated, it doesn't need any more explanation than that this is fiction and different artists render the same thing in different ways. Roddenberry himself liked to suggest that TOS was just the best approximation that they were able to manage with the available budget and resources, and that the underlying "reality" probably looked a lot better.
I believe McCoy explicitly says in Into Darkness
that the cryotubes are 300 years old? (An exchange along the lines of "We can't open the tubes." "Too advanced?" "No, too primitive.")