Option 1: The Shard of the Twelve Worlds wherein Dominaria formed a nexus with 12 other Planes that were locked off from the rest of the Multiverse. Perhaps Faerun is in a similar Shard to its Planes but locked off from the others.
That works particularly well as Feyworld and Shadowfells are echoes of the Material Plane (nexus) and in the same Shard.
Planeshift would only work to planes in the same Shard.
Option 2: The MTG planes are Demiplanes part of but locked out of the other Planes. So a Satyr does get shifted to the Feywild of Theros but thats a distinct demiplane in the vast Feywild. (Equally Innistrad and Ravenloft might both be Demiplanes in the Shadowfell and Innistrad also has its own Hell ‘echo’ thats distinct from the Abyss)
Option 3:Ravinica etc are Planes in the great Wheel, they are just more remote than the better known ones and as yet unexplored.
Option 4: Anything really
Option 5. All the MtG Planes are in a special crystal sphere which is filled with the blind eternities, and demiplanes are embedded in such as Ravnica, Theros, Zendikar, Amonket, Innistrad, Ikoria, Eldraine. They float around in the Blind Eterinites like the planes of Eberron do in it's sphere, but their is no central material world like Eberron, just an infinity of planes and the job of the Eldrazi is to make sure the crystal sphere doesn't get too full of planes as new ones are born, by eating the older and weaker planes.
Option 6. The Blind Eternities are a region of the Astral Plane that is more volitile then most and it produces crystal spheres. Even the Githyanki stay away from the Blind Eternities, only Eldrazi and Astral Dreadnaughts and similar creatures are crazy enough to explore the Blind Eternities and survive, well and those with a spark of the blind eternities inside them making them planeswalkers.
Material worlds linked to the Blind Eternities Astral Plane region, classified planes by the inhabitants of these worlds as they have every limited access to actual other planes like Aborea or the Abyss, although they have some access to Hell. They all have access to the Ethereal Plane, but they don't realize its a plane, they just wrongly think of it as being out of phase with the other stuff. There is also a Feywild, Shadowfell, and Elemental Border planes for them these worlds, usually although a few worlds might be created wrong by the Blind Eternities, so they are missing their natural mirror planes, or they are mutated, and they end up with extra ones compared to Crystal Spheres connected to regular spots in the Astral Plane.
Option 7 The Blind Eternities are actually apart of the Far Realms, hence why things like Eldrazi roam through it, but just as parts of the Far Realms taints the Material Plane and other planes, parts of the Material Plane and other planes taint the Far Realms, including the Far Realm known as the Blind Eternities, which causes it to create planes that resemble the material plane and other planes within itself. This is why the Eldrazi are destroying planes, they are actually as toxic to the Far Realms as stuff like Eldritch Horrors and Aboleths are to the regular planes, so ironically the Eldrazi are the good guys by the standards of the Far Realms blue orange morality.
Option 8 - D&D Ravnica and Theros are seperate from their MtG equivilants. Some Overgod like AO or another looked at a completely different multiverse, liked some of what they saw and decided to create an alternate, yet similar version in the D&D multiverse. Of course that would mean both the D&D multiverse and the MtG multiverse exist and while seperate, do have some kind of connection, being part of the same multimultiverse or Metaverse.
Option 9 - the Blind Eternities are a secret demiplane hidden within Realmspace, with Demiplanes within it, some of which like Theros have more demiplanes within themselves like those Russian Dolls that are inside of each other. This would make all the MtG planes apart of the Forgotten Realms. I expect this to be the least popular option.

Option 10 That WotC is going to have an IP shaking event that effects both D&D settings and MtG settings, that solves this and links them altogether. This really solves everything and could leave one of the other options as a result or something else. This is my prefered choice.