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> with Mlab you were able to specify the cloud provider and zone IIRC

That's correct, you specify a provider and region but can also set up VPC peering so all traffic remains within AWS' network within a region. I've used this setup - mLab on AWS with VPC peering and it worked great.

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But specifying the zone won't help since zones are not consistent across different accounts, so while you can ensure your in the same region, you may still end up talking across different data centers. Do they have anyway to handle this?

The same features exist in Atlas, so you should be good to go there.

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