I may be misunderstanding your question, but here's my answer-
1. In the Gygaxian Multiverse, all possible Eberrons are in the prime material plane. To the extent you want to "shut down" access from Eberron to other prime material planes (whether they are full planes, pocket planes, proto-planes, or, um, plane as the nose on your face....) you would just say that the borders are not porous, but nigh impenetrable. In other words, you'd have to ignore what is written as facially true, and instead view it as ... unreliable narration that gives you the gist that Eberron (and versions of it) are in the class of planes that are really hard to breach.
In other words- all versions of all words, from Greyhawk to Star Frontiers to Eberron to MtG to Mystara settings exists, but different worlds have different levels of "porousness" that allows people to go between them.
2. Or you just play it as written. Eberron is sui generis. Your campaign, and the Eberron cosmology around your campaign, is all that exists. There are no other settings or alternate worlds when you're playing an Eberron campaign.