To be honest, the "configuration is an executed .php file" system does make some amount of sense in the context of PHP. When your app has to re-run everything to serve a web request, having to re-load the config (especially if it's YAML, though JSON is less bad) is expensive. Re-running the PHP code, on the other hand, can be cached way better, in theory.

Of course, this is still all PHP's fault in the end: the core problem here is that you need to re-run everything to serve a web request, without ability to pre-load state like configuration.