First lets clear up a common misconception, the terms primary, secondary or tertiary DNS server does not imply that always the primary DNS server will be addressed and in case of failure, fallback occurs to the secondary DNS server etc.
On the OS, its just a list of DNS servers to choose from.
Usually there is some logic behind choosing which DNS server to query based upon for example network latency, number of network hops or just the DNS server thats quickest to respond.
When a client does a DNS query, chances are that it will take the path via the router's WAN DNS setting to get to Pi-hole for resolution.
From Pi-hole perspective, this query does not originate from the client but from the router and thus screwing up statistics on the web GUI.
If lucky, the web GUI will display about halve of the DNS queries coming from the clients an the other half from the router.
There is just no way to configure the Asus router in such a way that you get proper name resolution plus stats.
If you find one, please let me know 