The issue is that from Legion we learn that Elune created the Naaru, meaning she probably pre-dates azeroth and maybe the titans.The way I see it, Elune could be a secondary conscience of Azeroth, a defense mechanism, a part that's awake while the Titan sleeps and protects her. And she would be "installed" in these two massive Titan facilities: the moons. Apart from her influence on the natives of Azeroth, as she would have sent messages that the night elves interpreted the voice of a goddess, she would have some inert defenses that could aid us in the upcoming battle against the Void.
Similarly to how our Moon shields Earth from asteroids, these two would have been hit a few times by the Legion and the Void, perhaps one of them could even have an Old God that never made it to the surface of the planet. As a result, the Watchers of these satellites would have gone through a similar process as the Vrykul. Alien wildlife would have also populated them, possibly even some intelligent humanoid aliens who, after centuries of being stuck in there, lost the advanced knowledge that once allowed them to get there and became native tribal societies.
I've always found the idea of a hostile environment producing strong and resilient creatures to the point of them being a threat to heroes who have dealt with demigods interesting. The Timeless Isle and Draenor were that, and thematically they were great. Having this incredibly harsh place inhabited by powerful creatures and full of secret Titan technology right above our heads is a fascinating idea to me.