MC Server GUI will launch without starting the server so you will be able to set server specific launch commands. Under the Server GUI Tab there is a check box for custom launch configurations. (At the moment it is experimental.) You would tick the check box and enter your custom launch line. @dumptruckman added this feature just for those who had to run server specific launch profiles for their servers. Once you have entered your command line, go back to the main tab and click start.