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The difference is not in what is being done, but in who is in charge. If you modify your router settings, it's you. You decided that you are not going to honor

The difference is not in what is being done, but in who is in charge. If you modify your router settings, it's you. You decided that you are not going to honor ISP suggested defaults, and it is up to you to assess costs/benefits and pick the right choice. If Firefox overrides your settings, it means someone else does the decision about your tools. If that someone else makes it difficult to automate changing the default (e.g. ignoring DHCP; if you want, you can ignore DHCP at the system level, but this is not a decision an app should take), it means, that this someone else doesn't have good intentions towards you. Someone else decided what's "best" for you.

Spivak 8y ago
But right now within epsilon every computer will just blindly take what is given to it by DHCP making the local network operator, who is for almost everyone an untrusted party, the person who decides what's best for you. I agree that DNS should be a system level concern rather than an app-level concern but in the real world browsers want to protect their users' privacy and the OS they run on doesn't do that. If every app went out and started using app-level DNS then it might get annoying but browsers are particularly privacy and security sensitive. With this change almost everyone (i.e. people who don't mess with their OS setting and don't know or care what DNS is) are markedly better off.