I got killed by the Emperor and while I was going back there to get my stuff, the Emperor despawned (or at least disappeared). This caused the boss door to open.

The location of the impassable space:
Between -1218 163 -3613 and -1218 163 -3613 in the dungeon dimension on the Futurepack server.

EDIT:
I guess this is two is two issues in one:

1. The the invisible obstruction that was left behind
2. The Emperor should probably not have despawned in the first place.

This is a minecraft bug I cannot fix: sometimes the hitbox remains, even if I shrink it and teleport it away the world somehow does not update and you can collide with it. The despawning is strange thou.

I encountered the Emperor in another boss room. Since I could not kill it, I just started to leave, but the Emperor despawned before I could leave the dungeon, which opened the boss room.

I could not find an impassable space afterwards, but since I did not have my death marker mark his exact location, it might be that it exists, but I just did not find it.