Hey, I'd like to be able to override the caves with my own mod. From a brief look at the code, this doesn't seem to be possible.

I believe the change should be pretty easy. Instead of the following:

It would be something like

private MapGenBase caveGenerator = TerrainGen.getModdedMapGen(new MapGenCaves(), EventType.CAVE);

Let me know what you think!

Sure, why not :)
Will be a bit before it makes it into a release most likely, but you can grab a jar here for now:
https://jenkins.girafi.dk/job/Team%20Metallurgy%20Mods/job/Atum%202/job/Atum%202%201.12.2%20Jenkins/99/