About MySQL, to edit the port number and define the ips to access the server in the same LAN, in Ubuntu is used the /etc/mysql/mysql.conf.d/mysqld.cnf file. I used that file since long time ago, but in Fedora Server36 what is the equivalent?
In Linux configuration is generally in a /etc/config.conf file stored. Mostly there we do find a default config with all sections and comments to see what they do.
If an app has a .d directory this means you can just make changes for certain part of a config file and name it in a way, to give preference for execution and a description what it does.
A nice example is the file /etc/sudo.conf and the sub-folder sudoers.d
If the system has more than one user it is easy to make some additions and put them in the sudoers.d directory and name it as example as the usersname.
The directory is empty because you not made any changes yet. As explained above, it makes sense that you use the my.cnf as your default config, and put the changes in /etc/my.cnf.d/ . You even can separate them by domainname, webrootname etc.