I'm not certain I fully understand. Many raw changes won't prevent a save from loading, it mostly just happens if you completely delete an entry or move txt files around.
Completely new creatures don't cause the save to not load, they just won't appear because they have a population of 0 because none were created during worldgen.
Deleting a creature causes the game to not load because suddenly it has no information on creatures that already exists. Which it sounds like would happen with yer system anyway.
Changing a creature works correctly most of the time, just as long as the tag the game uses to identify it isn't changed. You could completely recreate almost anything from stone types to Dwarves, just as long as it still has the same header in the raw.
Changing a civ usually does not work because all those things are handled in worldgen.
If yer talking about seed compatibility, with new creatures civs will always be different because members will have gotten killed by different creatures that don't exist in the modded world, which would essentially change history. Serge lives to become a superpowerful fighter that saves the day in one world. But in another world Serge gets killed in his youth by a modded large carnivorous cat before he can become powerful.
With new materials they will be changed because an item could be made out of a materiel can end up being important to worldgen, changing history again, as well as the materiel itself changing the layout of the terrain.
Maybe I just misunderstood though.
EDIT: Chrono cross reference added