Where do I put configuration files for testing?
One way is to create a small testing module that contains specific config you need for a test, then have the test use it as a dependency. In my case, I put that module itself under the tests directory and marked it as hidden in its info file.

Although a drawback would be keeping these config files up to date when the system changes - but failing tests should point you in that direction too.

For Kernel tests be sure to call and install the test modules config.