After skimming over the code of Nullius I'm tempted to just flag it as incompatible with all of my mods.
It seems to blindly disable and hide almost all items, entities, recipes and technologies that don't start with "nullius-" in data-final-fixes.
There's 2 way for me to make mods work alongside Nullius:
1) rename my prototypes to "nullius-something"
2) overwrite its changes using dependency and data-final-fixes
Both are terrible hacks that I refuse to implement in any of my mods.
It should have a way for other mods to register prototype names it shouldn't touch.