Rather than the "fewest ingredients" and "non-standard ingredients" toggles I suggest a priority list: red, green, blue, purple, followed by mod packs. The user could have arrows to reorder packs (e.g. they've setup bobs module research but don't have purple yet). Functionally, it would prioritize based on the lowest-priority pack a research needs, not the highest-priority.

This would work better even for vanilla. Certain research items, namely Rocket Damage 1/2, need purple science but no blue science. Autoresearch thus considers them to be simpler than other research that only requires blue science, even though you haven't setup purple science.

It's a fair idea and I may look into something like this. I want AR to be completely agnostic about other mods, so I need a generic approach as I won't make specific code for other mods (such as bob's modules). I think this can be solved with a fairly generic approach, though. Just need to find the time to implement it :)

I found the time to implement something similar.
Instead of a setting for "Allow non-standard ingredients" I've added a way to filter out ingredients you don't have/want to be used in research.
This won't replace the "Fewest ingredients first" setting, though. That setting still serves a purpose.

I just saw this change in the new version. Great, this is exactly what we needed with the new research, or even with custom science packs like in Bob's modules.
Thanks!