Modern PHP applications use Composer to manage packages as well as to install PHP extensions. Configuring your PHP app is entirely for you to do - whether you keep your configuration in the database is not a problem of PHP, it's your applications and how it was made. These days I'd think the common thing is to just use ENV variables, like all other modern applications do. If you mean however to configure the PHP runtime, well yes, you have to touch php.ini for that, much like you have to have tons of flags to configure the Java runtime, I don't see how it's very different.
For PHP monitoring there are numerous modern solutions out there just a quick google search away.