Does ffmpeg have a configuration file?
No, ffmpeg does not use a configuration file post-install.

lots of ways to build ffmpeg, but generally you have to configure everything before install. 

for example, with brew (macOS package manager) you have to edit the following file to supply your --enable or --disable args BEFORE INSTALLING. 

/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/ffmpeg.rb

if you didn't get your args in on your original install, then you need to uninstall and re-install again with your desired options and args.

also: instead of supplying your options (--with-webp for example) from the CLI during install, you can write them in ffmpeg.rb.