I don't think there is away to disable content filtering for Site-to-site VPN traffic, you would need to make content filtering tweaks for all traffic. For the shop floor instead of using content filtering to block all URL patterns I would recommend using the Layer 3 firewall settings to deny any traffic, and then have L3 firewall rules to allow traffic to either internal subnets, or specific IPs/FQDNs. I do something similar on a bunch of networks I manage and it works quite well. As for your AMP issues, Meraki has mad a lot of improvements in the more recent firmware releases. What firmware version are you running on your MX appliances?
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