You are not going to be able to do that in a single Meraki organisation. Meraki requires all the subnets in any network that have VPN enabled to be unique across the entire Organisation. Even if you could deselect a site it would violate the unique subnet restriction. I have deployed a large number of Meraki networks and these restrictions speed up deployments incredibly, but mean you can't handle the small number of special cases like this. If it was me, I would put in a little ASA 5506 beside the MX at the special site to handle this case.
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