I also had this problem, but I believe it was caused by my having originally created the world using customised settings pre 1.13.
In any case, I had exactly the same warning message pop up every time I loaded the world in 1.16+ and also had the "legacy_biome_init_layer": true," line in my exported world generation settings .json. I found the location of the offending line using NBTExplorer inside: level.dat/Data/WorldGenSettings/dimensions/minecraft:overworld/generator/biome_source and simply deleted it.
Now the world loads without first presenting me with the warning message. Maybe this helps someone, idk