I looked at it, and it's harder than I thought. The actual code change is pretty small - if the level is the surface level, use my pond code, otherwise use vanilla code. But, I actually have to alter the vanilla class because most code calls it directly. That can't just be done with reflection, and is going to require ASM, which I have never done. So it's on my (large) todo pile.
I'm going back and forth on the issue or cheating back in the villagers and maps that got glitched out. Right now it's a low priority because they'll probably get glitched away again. Most likely if and when I get this solved I will cheat the stuff back in. You haven't seen this because it seems to be an interaction between RTG and Waystones. That's a bit odd because RTG doesn't change chunk handling after generation. Right now my best guess is that lighting problems are causing tick delays, and Waystones is not adjusting for them.