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It’s not that the Bunker wanted to change the floorplan almost literally every time anyone set foot in the bunker, the only solid place really being the entrance. It’s just that’s what it does. It confuses humans, or tries to, at the very least. The Men of Letters had adapted very quickly, as did the Winchesters and the assortment of humans, witches, angels, and demons that they kept bringing in. Oh, and the actual God himself. The Bunker isn’t sure how it forgot about God being within its walls.
God recognized it for what it was, and praised it for keeping so many people safe, as well as the wealth of supernatural knowledge that was invaluable (Sam Winchester may burn the library down if it doesn’t stop destroying his cataloguing system). It’s certain that the witch Rowena, the archangel Gabriel, and the demon Crowley knew what it was. And the Devil, Lucifer. Probably what it deemed “Asshole Michael” knew what it was, as well as that poor excuse for a Colonel Sanders demon.
It also knows it’s not the only one of its kind roaming this earth, whether that be an eldritch being like itself or an elemental, like the one that haunts Leap Castle in Ireland (the Bunker tries to refrain from talking to It, just simply because of the putrid smell that It tends to emanate. The Bunker may be styled like a Cold War era doomsday bunker, but at least it doesn’t smell like rotting flesh. However, that could also be due to having been summoned to a castle with a very blood drenched past).
The Bunker also liked humans, an oddity among its kind, and was more than willing to provide Sam and Dean Winchester, and the angel Castiel and now, the Nephilim Jack with what they needed. As well as their mother, Mary, and Bobby, it supposed (it wasn’t a fan of these two newbies, but its not sure if it’s because one is supposed to be long dead and buried and the other one is from an alternate timeline, or if it just has an irrational dislike to them. It doesn’t question its motivations).
Well, as much as they can.
It just hopes that once Sam has organized the library to both of their liking, the younger hunter doesn’t then try to map the floor plan. That may as well make Sam lose his mind, and the Bunker liked Sam too much for that.
As long as its charges were in its walls, it knew that they were safe.