I understand that. But if in the Prime universe in a series episode the ship in question is voluntarily flying around in the atmosphere then no matter what a website says about them canonically they can fly in the atmosphere. Ergo, the NX is atmosphere flight capable so Beyond having an NX do it is not outside canon.
Now Into Darkness having the ENTIRE Enterprise acting like a submarine? That tripped my canon sensor too!
Well, that is a very loose interpretation of "flight" for a starship isn't it? Lets go further and say also that any object in space which enters an atmosphere is capable of flight, even if it is plummeting to the ground. It's still flying through the atmosphere! The saucer section of the Enterprise D in Generations "flew" to the ground in a crash landing in the movie. So, Galaxy class starship saucer sections can all "fly"?
Im just not so willing to let all that stuff slide through and say nothing about it. That does not make me right or anything, just a purist. Technically, the saucer separation in TNG was a Johnny come Lately. That saucer should have been able to land on a planet like Roddenberry himself originally intended. He was in charge still, when the first saucer separation scene happened in TNG, and he did not take the opportunity.