I don't see all the tunnel/MEP management options for the pre-built "RemoteAccess" community so it seems that based on this statement:
Officially, MEP is only supported when the Security Gateways have completely overlapping Remote Access encryption domains, and Secondary Connect is only supported when the Security Gateways have completely separate Remote Access encryption domains, with no overlap at all.
When there are "partially overlapping encryption" domains, the configuration does not fully fit the MEP, and also the Secondary Connect Encryption domain requirements. Therefore, this warning message pops-up in order to warn the administrator that it might affect the use of these features.
To prevent this error message and not to affect the MEP and Secondary Connect features, avoid configuring partial encryption domains inside the Remote Access community.
... all I would need to do is ensure both gateways have the exact same encryption domains?
This would be OK except they both have a unique VLAN on each side as well. I suppose mixing the two is whats not supported.