You'll be able to create the non-Meraki VPN using whatever subnets you want.
However the routing table will control where to send traffic. If site 'A' is advertising a subnet via AutoVPN to site 'X', then site 'X' will send traffic for that subnet to site 'A' rather than any remote non-Meraki VPN.
You will need to stop advertising into AutoVPN any subnets that you want site 'X' and 'Y' to be able to access over their non-Meraki VPN.