Hi again.
The second setting for allowing waterfill to be placed over tree stumps appears to be unneeded, since they will be removed either way (I think there was a game update with a fix a long time ago). But when the setting is enabled, grass and other decoratives often end up covering water tiles on map generation, because the property doodad=true within the data.raw.tile.water.collision_mask.layers table is missing.
I have testing things, and it seems better to just get rid of the setting entirely! But leaving it off for now works as well.