Being a god of one territory doesn’t stop you from using another one. The titans are the arcane pantheon but they’ve used water and lightning (Golganneth), nature (Eonar), and fire and earth (Khaz’goroth). The Winter Queen also uses nature despite being part of the death pantheon.
Elune having used other types of magics doesn’t mean she isn’t a Nature Lord or whatever, which is what it feels like they’re going for when the Winter Queen calls Elune her sister.