Amusingly the suckless package suite does exactly that, all your configuration is done in native c as a large array I believe and compiled into the program.

Also most Freeware daemons and servers are configured by running a literal bash script when they start.

That being said configuration files exist because not everyone knows BASH, or C, or Python, or Javascript/Node.js But also every software developer doesn't want to spend a week or two making a configuration GUI.