Hello @Aileron87
The Meraki Go platform, as of today, does not support site-to-site VPN. You may be referring to the enterprise line of Meraki products.
However, to answer your question, the site to site VPN firewall rules on the enterprise line are organization wide. That means every MX will interpret them globally. So if site A sends traffic to site B but site B has firewall rules, the traffic will still be subject to them as they are global to all MX in the site-to-site VPN topology.
Looking for the Cisco Meraki enterprise community?