New generation rewrite introduced 18w06a have caused many weird things. Upon loading up a world to see the new changes for myself I spawned instantly looking at a floating water stronghold.

However, this happened only one time. I ended up generating the world three times, and only the second generated world (that was done using the re-create feature) had missing blocks. making another recreate based on the original one and the broken one kept the stronghold in shape.

Again, not exactly sure what the cause is. I have a hunch it may be related to the direction I spawned, since the broken portal had me spawned facing away from it, contrary to every other time I generated the world.