I agree that it would be nice with support for modded ores/fluids, I'm also thinking especially about Krastorio 2.
It can be done in a simple way and in a complex way. Luckily, as it usually requires more technology to process the advanced ores/fluids, you could just add one recipe for each type of ore.
However, as you seem to at the moment have one recipe that gives many ores, it might be a bit more tricky to automatically group them up, but it could be possible. For example, you can estimate how complex something is by checking how deep it is in the technology tree and group similar ones in the same recipe. Didn't say it would be trivial, but it's possible.
Naturally though, manual support for specific mods (Bob's, Angel's, Krastorio 2) is probably the best approach to make sure it's properly balanced.