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Sorry for all the confusion, its a great portrait pack!
At least my quick test ( with use of console commands) does not show clear symptom.
Have you try the Alter Crystalite? It should acted as normal lithoid.
Anyway, my alternative solution is to mimic my "Alternate Neptunia and Anime Girls Portraits".
Move portrait files into that and leave custom trait on other mod.
As for portrait, I did add "Alter Crystalite" as separate species class without modded trait.
I really don't want to create separate mod. Too much trouble updating.