Internal commands are commands that Multi Commander or an Extension or Plug-in has provided. For example, the menu and tool bars use these commands. They are simple commands that just tell Multi Commander or the Extension that the command has been called, and no parameters or customization for that command can be added.
One reason to create a User Defined Command that uses internal commands is to create an alias for that command so you can call that command from the command line bar. Another use would be to assign that command to a button on the button panel.
The command might also be something that is not normally visible in the menu bar, but you would like to put it there. In this case, you can create a User Defined Command that calls the internal command, then add the User Defined Command to the menu bar using the User Menu Configuration.