DNS Server field is the DNS server router's system will use, it's should be set to a reliable one.
It is used for time sync, DDNS and few other things.
So setting AdGuard's DoT server details in the DoT list is the way.
As far as I can tell it works like this:
WAN->DoT is disabled, no custom servers set in LAN->DHCP:
Router will advertise itself as DNS server and forward all DNS queries to servers set in WAN->DNS Server
WAN->DoT is disabled, custom servers are set in LAN->DHCP:
Router will advertise DNS servers specified in LAN->DHCP
WAN->DoT is enabled, no custom servers set in LAN->DHCP:
Router will advertise itself as DNS server and forward all DNS queries to servers set in WAN->DNS-over-TLS servers through Stubby
If servers set on that list are not IP addresses then they will first be resolved to IPs using a DNS server set in WAN->DNS Server
WAN->DoT is enabled, custom servers are set in LAN->DHCP:
Router will advertise DNS servers specified in LAN->DHCP
While Stubby is configured and launched in this case - the clients will never know about it