In Pathfinder, a creature by default occupies a 5 foot by 5 foot square, a 10 foot by 10 foot square, a 15 foot by 15 foot square, etc. The space is always a square. But the creature is almost always physically smaller than the square. (The gelatinous cube does fill its entire square.) The square around a creature, such as the 5 foot by 5 foot square around a human, includes dodge room. Thus, creatures can squeeze into smaller spaces that are not too small.
For example, a hill giant that occupies a 10 foot by 10 foot square could squeeze into a 5-foot-wide corridor. The GM might rule that it is denied its Dexterity bonus to AC because it lacks room to dodge, but it can get down that corridor. Other creatures might fit better. A horse is considered a Large creature, so it takes up a 10 foot by 10 foot square, but horses are long rather than big in all directions, so they can go down a 5-foot-wide corridor without squeezing.
Since the ghelarn is an animal that lives in a mobile shell, much like a giant snail but with more tentacles, it probably crawled into the tunnel labeled B6 as further protection before it went into hibernation. Thus, it intended to pull its shell pieces tight around its central body and would not mind a snug fit. It is up to the GM to decided how much AC it loses due to lacking its full dodge space around it. Maybe none, because it might simply be a smaller-than-average ghelarn.
And this is the correct subforum for questions about unique creatures in the Iron Gods adventure path.