I agree with these two. That doesn't look like Cupcake.
It's the same actor (Jason Matthew Smith). He just ditched the goatee and let his hair grow out some.
Smith was credited in the end credits as "Burly Cadet #1" in Star Trek XI and actually as "Cupcake" in Star Trek XII (despite being addressed onscreen in the latter as "Mr. Hendorff").
You're correct concerning the credits, but I think
mattman8907 and
Set Harth are also correct in saying the large redshirt behind Cumberbatch's left shoulder in the scene which has Khan being escorted by the security detail does not look like Jason Matthew Smith's Cupcake. Compare the image accompanying
this article (different camera angle than the shot provided upthread) to Cupcake/Hendorff's appearance during the
chase scene. They're not the same actor.
[Edit: the large redshirt in the security detail scene is probably
this guy - he played the
large alien cadet in the last movie.]