By default, Medis doesn't use your SSH config file located at ~/.ssh/config due to the restrictions applied by Apple sandbox, which is a mechanism aiming at protecting your files. Simply put, the mechanism is that the application can only access files that the user has manually selected in the program.
If you don't select your SSH config file explicitly, Medis uses an empty SSH config file. You can select your SSH config file in the application preference.
Note that if you are using the App Store version, you will also need to grant Medis access to files that are needed by the SSH config, for example, identity files, with the + button below.