config: Omit writing values if they are empty

We are generation a configuration file when we want to run praefect for the testing purposes. The issue is that we are generating a file with all values even if they are not set because we are not using omitempty option for marshalling. With the option set the setting won't be included in the resulting file in case it is has a default value of the type.

Closes: #3304 (closed)