Yes. You can launch Crazy Num Caps Scroll directly from the command line to skip the configuration screen:
/c{seconds} -- Toggle Caps Lock at the specified interval
/n{seconds} -- Toggle Num Lock at the specified interval
/s{seconds} -- Toggle Scroll Lock at the specified interval
Example: CRAZY_NCS.EXE /c5 /n10 /s25 toggles Caps Lock every 5 seconds, Num Lock every 10, and Scroll Lock every 25.