I think the Section 31 agent at the end of the comic is Number One. That's why we didn't see her face--it would have been recognizable.
Why? Nobody else's is. Although some of the guest characters in the comics have looked more or less like their Prime counterparts. (I found it odd that Commissioner Ferris had a new character design in the early pages of the "Galileo Seven" adaptation but then looked just like John Crawford in the rest of it.)
Hey, I wonder if they'll make a thing out of the fact that Number One looks a lot like Christine Chapel.
Again, no reason they should. If they have different-looking actors playing characters who look the same in-universe (Spock Prime recognized young Kirk and Scotty on sight), then by the same token, different characters played by the same actress may not be intended to look alike in-universe. Actor resemblance (or lack thereof) should not be mistaken for character resemblance, unless it's specifically referenced.
Besides, remember that "The Cage" was filmed only 2 years before the series proper but set 13 years before. So Number One would've been about a decade older than Chapel.