Alternate DNS resolution for Safari on macOS?

It sounds like you've done a pretty good job of covering all of your bases... as far as IPv4 is concerned. Maybe it's IPv6 that's causing you headaches? I believe that disabling IPv6 on the connection will fix the problem. IIRC IPv6 can autoconfigure itself without DHCP. If the rest of your network works with IPv6 then the queries could still be working over IPv6.

You should try setting up a "Location" from System Preferences--> Network. Then, for that location, go to Advanced...DNS Servers for your network device (eth0, Wi-Fi, etc) and point it at your Pihole device. You need to specify both an IPv4 and an IPv6 DNS server.

From the same panel, if you click TCP/IP, you can confirm which DHCP information you're using and disable IPv6 (change it to link local only or manual with a bogus address).