Ok, I discovered a lot more interesting information:
- base Factorio defaults to letting you landfill just water and deep water (including green)
- Space Age adds mud/marsh/shallow water as well as many Gleba-specific marshy tiles
- Alien Biomes adds mud/marsh/shallow water, as mentioned above since v0.7.1; this is good because AB enables terrain generation of those tiles
So to reproduce the problem I had to install AB, generate a wet world, and then disable AB and SA both, at which point my quick hack of a mod fixed it. I will publish shortly.