Assuming your MX's are the L3 gateway between the client devices and internal DNS server(s) - Wouldn't the DNS query and response to/from your Internal DNS server(s) still be observed by the local MX and therefore qualify for inclusion in DNS-based VPN exclusion rules?
As an example, if we wanted to exclude www.google.com from the VPN full-tunnel to Secure Connect:
1. Client PC makes a DNS query to for www.google.com to Internal DNS server
2. DNS query transits local MX where VPN tunnel exclusion is configured for FQDN www.google.com
3. Internal DNS server responds to query with IP for www.google.com (let's say IP 1.1.1.1 is returned in the query response)
4. DNS query response transits local MX where VPN tunnel exclusion is configured for www.google.com - local MX observes 1.1.1.1 provided in query response
5. Local MX adds 1.1.1.1 to VPN tunnel exclusions based on observing the DNS query and response
The DNS query and response must not be encrypted otherwise the local MX will not be able to see query and response details within the packets
A quick method I use to validate if DNS-based exclusion rules are working is to perform a traceroute to the FQDN after the first DNS query is made - you should see the trace following a path into the local WAN provider rather than into Secure Connect
I also believe that Meraki support are able to see/query the IP's that are added to VPN full-tunnel exclusion list by DNS-based rule configuration