DNS settings will sometimes be ignored

I've noticed that my DNS settings are sometimes being ignored. When I checked my logs, I realized that some requests were not sending the device name, despite making sure it was set up correctly as per the instructions on the setup page. Upon using dnscheck.tools, I discovered that my system was utilizing various DNS servers that I was not aware of, instead of solely relying on NextDNS. After extensively reviewing all network settings for potential issues, I found nothing that could explain this behavior. I then experimented with YogaDNS and found an option called "Intercept DNS packets injected by third-party filters," which effectively resolved all the aforementioned issues. My question is, how can I achieve this without having to rely on YogaDNS?