The point is that your router is a client of your ISPs network and you're overriding the servers provided by DHCP to your router.
In a crazy world where internally Firefox ran a small IP network for each tab and routed traffic between them for IPC would it suddenly be okay for Firefox to override DNS? Why or why not?
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.
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.
"You can configure your router, a client device, to use whatever DNS server you want in defiance of your ISP, a network operator."
Which one do you want?