I wonder if this broke the pyramid on my side. Now reading the log I guess it has on the bottom stone chest portion hmm (view the 0.8.2 help thread).
Well, the pyramid spawn was problematic. In some cases the pyramid was placed at a proper elevation, but obviously in some situations the position of the pyramid was completely wrong (far too high, like in your case) 
It gradually got worse, with the worst part being when I had to travel back 18 min back to my other spawn settlement
Yeah, noticed it when I was looking for broken pyramids in my world
Returning to the main menu and reloading the world usually did the trick. However, it should be solved now, at least I was able to fly around for more than 30 minutes without any performance issues 
Curious about what happened with the pyramid I have going on with what's happening at the chest room. It's just a void.
It looks like the world conversion does not work properly for dungeons. I wasn't expecting this... I'm still looking for a suitable solution, in the future it's anyway necessary to fix the dungeon world converter (it's unacceptable that worlds break everytime now if a new dungeon gets added), but I'm not sure if there is a chance to rescue existing worlds 
Edit; It is because of the pyramid fixing that the pyramids all moved around, even glitched out if you claimed them
Yeah, a faulty world converter in combination with edited chunks is really problematic
Once a chunk gets edited (block removed, placed etc), it gets stored to the database, so this state definitely stays. That's why your pyramids are now broken, I'm sorry for all this hassle
The easiest way to get rid of the blocks is to use the creative mode now (F6 -> 2 [block placement] -> select all blocks -> hit the DEL key to remove them all at once)...
Yes, I get the performance thing, however different types of terrain may absorb water quicker than others for instance. Sand almost instantly, rock not so much. Also maybe it could be a feature that can be turned on and off for a world, noting the huge performance hit?
I really can't say much about that yet
Calculating these things is quite expensive (in terms of performance), especially if a server has to calculate this at several position simultaneously. On the other hand, it would be a pity if such a feature was only available in singleplayer for example (especially since it would take some time to implement it). Well, we'll see how things finally turn out 