Ilphyl does notice that their companion does not actually need to breathe -- elf hearing is sensitive. As soon as they hear the troops come down the tunnel, they tap Atom's arm as a warning -- no one likes a sudden light, and they cast their spell with a few words and gestures. The lights look enough like lantern light they could be mistaken for a small group with lanterns from a distance.

As soon as the spell is set, they are already starting their wild shape, shifting into a large black-and-white rat while holding the spell.