Following up:
I attempted another run to gather more information, this time with no modifiers set, but after finishing the last room in the 4th area it functioned normally.
I am uncertain if this is because the boss can only be encountered after the restoration cutscene, or if it's because of the modifiers I had been using.
In case it's because of the modifiers, I have included the list below.
Modifiers:
Reduced Stamina 5
Reduced Healing 5
More enemies 4
Reduce Arcana 5
More elites 0
Shielded enemies 5
Time limit off
No shops on
More minibosses on
Less healing items 2
Sadly, in the course of testing I found another portal outside the valid play area in world 3.
It spawned on an inaccessible mesa, just below a flesh tree and next to a decorative hole.