If your ISP provides DNS servers by default, Microtik will use them even if you have a custom DNS server.

Doing a /ip dns print will show this in dynamic-servers field:

1[admin@ATik-Pro-1G] /ip/dns> print
2servers: 1.1.1.1
3dynamic-servers: xxx.x.xxx.xx,xxx.xxx.xxx.xx <--- From ISP
4use-doh-server:
5verify-doh-cert: no
6...

To disable this completely, set use-peer-dns=no on your WAN interface's DHCP client:

1/ip dhcp-client set 0 use-peer-dns=no

Results:

1[admin@ATik-Pro-1G] /ip/dns> /ip dns print
2servers: 1.1.1.1
3dynamic-servers:                             <--- No more!
4use-doh-server:
5verify-doh-cert: no
6...

This will ensure your custom DNS server is always used, instead of your ISP's.