See, I've been reading it as a collection of realms and spirits, which are associated with one side or the other, and certain places overlap. Like the White Lodge and the Black Lodge are two kingdoms, with some sort of hierarchy attached to them. As we've seen, the Arm seems to be the highest authority in the Black Lodge, and the Fireman the highest authority in the White Lodge. There are associated spirits and realms. I saw the Purple Sea as an outer realm of the White Lodge, and the Mauve Room as another associated realm. The Fireman's stronghold is at the top of mountainous island, it's the highest and deepest part of the White Lodge. The Red Room is part of the Black Lodge, but seems to be the part where spirits from all alignments can visit, analogous to the Purple Sea or the Mauve Room (which seem to be on the same island, only lower, than the Fireman's stronghold) while the darkened rooms Cooper visited during his test were deeper in the Black Lodge.
The convenience store seems to be a Black Lodge realm but not the Lodge itself, and so does the shadow of the hotel that Doppelcoop visits to talk to Jeffries. However, I'm not 100% convinced Jeffries is there. The wall disappears, and Jeffries appears to be inside a device shaped like the sorts we've only seen in White Lodge-associated rooms, with a wall that appears like a White Lodge associated room. I suspect Doppelcoop was talking to a projection, and the Inn may be a place where the realms can cross.
Either way, did anyone else play White Wolf World of Darkness RPGs when they were younger? There's a concept in Mage/Werewolf/Wraith and arguably Changeling that comes to mind. The Umbra and the Dreaming. Both are spiritual realities that shadow the real world, resembling it very closely when you initially cross the barrier but becoming stranger and wilder as you get farther from earth. The Umbra has the Near Umbra and the Deep Umbra and there's a whole area that's basically just a warped shadow of Earth, while the Deep Umbra has different realms with different rules. I've been thinking of the White Lodge and Black Lodge as like a combination of the Umbra and the Dreaming, and seeing the motel just made that interpretation stick even more. The motel is clearly a warped shadow of that physical motel, while Jeffries seems to very very deep in this other dimension. The convenience store also seems like a shadow of the physical world.
The Red Room doesn't seem like a shadow of the real world, though. It's distinct. It's well-kept. It's more solid than the places the Woodsman are. The Purple Sea and the Mauve room don't seem as solid, but they seem as distinct and as original as the Red Room. They don't seem like places that are a copy of other places. The place above the convenience store seems otherworldly, but earthly. Like it's just a shadow of Earth rather than a full part of the Lodge dimensions.