I first noticed this with Occultism's "foliot ore crusher" summoning ritual, which requires raw silver. This appears to be the only ritual which requires raw ore, but summoned ore crushers are the only way to get crushed end stone, which is required for the mod's progression. There are ore crusher summoning rituals which don't require raw ores, but all of them require purple chalk, which is made from crushed end stone.

This seems to be an issue with the way AllTheOres tags the raw ores.

Occultism raw silver and ImmersiveEngineering raw silver both work, and they are are tagged #forge:raw_ores/silver. All of the raw ores from AllTheOres are tagged as #forge:raw_ores/raw_xxx, while the vanilla raw ores (as well as the Occultism and ImmersiveEngineering raw ores) are all in the format #forge:raw_ores/xxx.

This also appears to mean that all non-vanilla raw ores cannot be crushed by any means except the AllTheOres ore hammer. So ImmersiveEngineering's crusher can only be used to duplicate non-vanilla ores if you use the ore block itself via silk touch.

The only workaround I've found for the Occultism issue has been to use console commands to exchange types of raw silver ore on the honor system.

Oops! It looks like this was already updated and fixed since I downloaded the pack the other day. My bad!