I've noticed a few kit-related issues after installing Nephele in BG2:EE. Her list of proficiencies during level up doesn't display any allowed weapon proficiencies and styles. Moreover, I've also noticed that she doesn't get any further proficiency points during level up.
Also, her record screen and class description are that of a vanilla cleric. She still has her kit-specific special abilities however and her initially set weapon proficiencies appear to work fine.
Some screenshots to depict these problems:
There's another minor issue I've noticed in both BG2:EE and the original BG2 (although I'm not sure whether it's intentional or not). Her initial equipment includes a Ring of Protection that is still in an unidentified state.