Before destroying the support pillars and causing the fourth floor to collapse onto the third, the four rooms in the center of Eagle's Tower's third floor are entirely different, consisting primarily of an extremely large pit. Of these rooms, the upper two are inaccessible and never normally seen in-game. It appears the one on the left was meant to be used, but due to the way the crystal switches work, the blocks controlled by them will always deny you entry. And even if it was accessible, the pit is too open and can easily lead to getting trapped on the second floor. Interestingly, while the room is inaccessible, it was still updated after the first version.

To the right of that room is one that was definitely never intended to be used at all, consisting only of a "down" staircase leading up to the fourth floor, presumably for testing purposes. It's also the only way to get up there. (Leaving the 4F area in any direction will take you to blank "default" rooms.)

These rooms are also present in the DX version.