Can you update the water outside of the data stage so it can't break anything else?
That is the only request, Leave vanilla stuff unmodified for the data stage alone, and then do what you want afterwards.

I modify it in the data stage so you can undo that change in the data-updates stage if you wish?

Honestly perhaps I should go back to having my own custom tile - it took HOURS trying to figure out the placement logic of water tiles which appear to act very specially when allowed to spawn verse other ones.

I'll have a look at what you can do because 100% I didn't want to be altering the vanilla tiles, but still wanted to use them for the Halo generated (tricky!)

Just don't do it in the data stage, because that prevents everyone else from doing anything with them. (:
Updates is fine for these, it gives everyone else a way out. You can modify it, just leave a little room for everyone else.

It looks like it's specifically the empty-space tile's probability that is causing Dea Dia to break (not any of the water tiles).

I'd suggest if you really need the generation, particularly for the tiles that don't normally have it, just make your own copies of the tiles and use those (the tile limit is 65535 now), particularly since the foundation and space-platform-foundation tiles also seem to be in use by a few other mods. That way you can keep your probability expressions without clobbering any other mods that are making use of them.

This looks like it could be a lot of fun, and can't wait to see where you take the mod!