Many times variant covers are commissioned and even completed before the entire story is fleshed out and written. I pitched concepts and had the series moved forward I would have talked to both IDW and Dark Horse. But there was a scenario running through my head when I did the sketches: The Enterprise is compromised by Xenomorphs. The ship was being evacuated and a self destruct was ordered. Spot, of course, escapes and tries to run back to her cabin. Data would have rushed back, probably fought off an attack and rescued her just in the nick of time. (Yes, a call back to Jonesy from Alien) Would the ship have exploded? Probably not--again this was semi-detached from the story which would have included Romulans and Borg assimilated Xenomorphs.
And "Is there an in-story reason why it's so dark throughout the Enterprise?" it's red alert and they are on emergency power - I had 2 versions of each cover one with the red lights all on and then ones with fewer which seem 'brighter'