Things worked better when Elune was mysterious and most of the races religions / deities were on par with each other. Having almost every race of the Alliance some sort of titan construct derivative, chosen champions of the Naaru, and now chosen champions of some sort of other prime god, while most of the Horde races just kinda exist and at best are tied to nature gods or lesser elementals is kinda dumb tbh.
And even putting aside faction disparity, it kinda further homogenizes the Alliance. Great, now you’re all some sort of weird cosmic divine servants except for the Pandaren (who don’t matter b/c they’re split between factions). Because when everyone is special no one is special.
As for how it relates to the Horde story, well there’s a few ways this can pan out, none of which are good.
-The Horde simply doesn’t exist in the narrative anytime this comes up and its champions are neutral again (As done in Legion).
-Somehow, Ana’she is part of Elune and the Tauren got her name wrong all these years, or something similarly forced.
-Nelves are effectively neutral again due to the Cenaurian Oval, Ellipse, Dot, or whatever new derivative of the CC we’re stuck dealing with again.
-The story goes out of its way (inadvertently or deliberately) to hammer home just how wrong the Horde player is for not believing in the Nelf goddess.
Main pint being, maybe it’s a mistake to have the only connection for the player races to the supposed first ones be a very race specific racial deity, because it now has to be homogenized and watered down for everyone, or it screws over the races who aren’t deemed as important.