When setting the Site-to-Site VPN settings on MX-1 to spoke or hub, it will begin to participate in the AutoVPN topology between MX-2 and MX-3, assuming all three MX's are in the same Organization.
I'm not sure if you can have Meraki Support disable AutoVPN on MX-1 in the backend. You'll have to open a case, to clarify that.
However, I'm rather certain that if you do not enable subnets on MX-1 to participate in the AutoVPN, these subnets will not be advertise to MX-2 and -3. However, MX-2 and -3 will advertise their subnets to MX-1. So you'll still need to have unique subnetting on all three sites. As long as you have the Private Subnets configured in the VPN configuration for your peer, as well as the other way around, it should be OK.
When configuring Non-Meraki VPNs, the configuration will be organization-wide, meaning that MX-2 and -3 will also being to initiate a VPN connection to your peer. However, you can control this by using Availability tags. Tagging the Network that should have the Non-Meraki VPN, and setting this tag in the Availability field on the VPN configuration, will ensure that it will only be MX-1 that initiates a VPN to your peer.
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