In addition, every additional setting multiplies the number of states your application can be in, and the combinatorial explosion of states is mostly not well-tested. If you set even a handful settings to non-default values, it's likely that you are running the application in a totally unique configuration that's not used by any other developer or user. If you encounter bugs, you're liable to get the "Idk, it works on my machine" response.

This blog post also covers other good reasons why user options are often not the right choice: https://garethrees.org/2013/06/13/options/