DTM File Factory supports following command line switches:

-r - if project configured, run the project at program startup

-q - quit the program after project execution.

-c - console mode.

The console mode is a mode when the program doesn't open any dialogs and doesn't need any interference from the user. A project for the console mode must be prepared and tested beforehand.

Also, you can use project name as a command line parameter. Please note that you should use quotation for path or filename with spaces:
ffct.exe "D:\Projects And Files\messages.ffct"