And yet, they had Dalet and Aleph. Point stands: I don't know how much more identical you can get than identical, but those worlds were identical to Bet with exception to Scion. So your conclusions are wrong. Also note that Scion never wanted them to access those worlds, of course. Power interaction, and Entity Attention Failure. It was just a reason why they were almost the same as Bet, yet didn't have paras of their own (until the gateways were made). While other, nonsimilar worlds, DID have parahumans.
Realities were partitioned off, yes, but not sealed off. Not like the Zion-body-world was sealed.
Also: what you have listed as spoilers for atonement are from Silencio. So, y'know, whatevs. I read both. Up until the point where I dropped Atonement on the grounds that it was boring, predictable in its desperate attempts to be unpredictable, annoying, and just generally lacking in redeeming qualities.