In the novel, it is clear from the start of the mission that Quenser and Heivia have not been deployed alone and are instead part of a group of over a hundred soldiers sent to take out the terrorists in Antarctica, unlike the anime were the other soldiers are only seen after the base is captured by the 37th. Just before meeting the spare secondary railguns, Quenser is close enough to his allies to exchange a wave with a fellow soldier. The railguns also fire at all Legitimacy Kingdom soldiers, not just Quenser and Heivia.
The penguin scene occurs quite differently in the novels; a single baby penguin wanders into the middle of the firefight, causing both sides to cease fire and start watching its progress. A seagull appears and momentarily threatens the baby, but the baby penguin's mother appears and manages to drive back the seagull, causing both sides to cheer wildly at the familial love. Disturbed by the loud cheering, the mother takes the baby with her and starts walking away, with the firefight not resuming until after both penguins have left the area ten minutes later.