I think part of the issue is that the Raven Queen is a goddess in Nerath (and even may have given her name to the nation itself – the capital is named Nera, and one 4e legend of the goddess claimed she was originally the consort of Nerull, an ascended human who became the winter goddess Nera, until she overthrew him and took on his death portfolio). Meanwhile, she had NO official role in the Realms.
She's an official goddess with 4e-type lore in Exandria, so I think we can take this as a bit of evidence that there's 2 different Raven Queens in 5e – the former Human Goddess (in DMG & EGtW), and the Elven interloper (in MTF), who are present in different settings and have different roles in their settings.
This suggests to me that the Crystal Spheres of old may still be in place, rather than one set of Planescape planes for all D&D settings (should have been obvious due to Eberron and Magic: The Gathering having different cosmologies, but there's been some questions of this in these forums).