I was able to fix the issue by setting up a DNS server on the WireGuard server which returns the WireGuard server’s internal wg0-vpn IP address (10.0.25.1). I then patched /etc/init.d/wireguard so dnsmasq switches to using /tmp/resolv.conf.vpn when the VPN becomes active and back to forwarding to Stubby when the VPN connection is shut down.
More details and a patch are available at Wireguard client not honoring DNS setting [workaround discovered] - #14 by crahan