The console app output does not use the Application or User options (although this is on the todo list), but the log file output uses the App log settings whether built with the console or GUI app.
You can copy the console app to another folder and run from there. See here for where the application options get loaded from (the config file won't get created until changes are made to app options and VBP exits).
http://www.kinook.com/VisBuildPro/Ma...ationfiles.htm