cephalo
Deity
I haven't messed with floodplains yet so maybe I can take advantage of your testing
It sounds like placing floodplains via the "old" method in featuregenerator.lua makes floodplains that give the old food bonus but don't actually flood, is that correct? If so that's actually kind of cool in a way, but unfortunate that we can't fully re-write that placement code for ourselves. Did you see if floodplains placed that way allow for the dam to be built on them like the new floodplains? I'd actually be curious about testing for their presence in a tile (the new style floodplains) since they appear to use the same feature ID.
I'm guessing there's an underlying database that is separate from the actual tile data, similar to the river naming scheme. It's unfortunate they couldn't fix all this stuff up after a map is generated, but I suppose it's not a small task. One disadvantage to this is that the default placement will not overwrite any features, but if you run the floodplains first, you get floodplains everywhere. I would not be surprised if you subsequently replaced the fp after, if the tile would not still flood anyway, but I have not tested that.