Using unofficial beta 1 for 1.12.2. Seems to happen also when simply disabling dusts. alternatives exist in my pack to the dusts so recipes are not broken afaik.
Crashlog:
https://gist.github.com/Voxel-Friend/65b730092d3f066941aaa8d66173f94a

The logging of list parsing is now greatly improved and, as of my cargo blacklist commit a couple weeks ago, no longer crashes on invalid lines. Rather it logs them as an error and ignores them.

Will make the config fail-safe instead. Moreover, note that once you disable a module, you have to change many related stuff, especially advancements and loot tables (loot tables will yield nothing if one of its entry is in a disabled module)

Is all that configurable in the config?

See https://minecraft.gamepedia.com/index.php?title=Loot_table&oldid=1115017#Custom_Maps
The loot tables are changed in vanilla ways. For railcraft, change the <custom directory> part to railcraft (must be all lowercase). A few are available here at https://github.com/Railcraft/Railcraft/tree/mc-1.12.2/src/main/resources/assets/railcraft/loot_tables/chests . For example, you will refer to the simple_dungeon.json with data/loot_tables/railcraft/chests/simple_dungeon.json

For now to stop the crash, remove the dusts from the list of worldspike fuels. I bet you need the void dust for worldspikes to run.

For the advancements, see https://minecraft.gamepedia.com/index.php?title=Advancements&oldid=1151757#JSON_Format

Thanks!

After discussion, we decided to crash with a clearer message instead.

At the very least it needs to print which file and setting failed.

Well, I just made a mod for that purpose. https://github.com/liachmodded/datapacks/

I kind of figured we'd just hardcode it into the parser call.