(Sorry for my poor english)
Raptor.exe is like a "Wrapper" for rapwin.exe and located in the installed directory. It's possible to start that rapwin.exe to avoid that Config-Dialog.
Unfortunately, if you start the game this way, it won't use the settings that you have done on the Config-Screen - the Game will just start on window mode, 640x400, without HQ-Filter and Keyboard-Controls.
The solution is: rapwin.exe can handle Parameters at start.
What I have found out, rapwin.exe can handle those Parameters:
Set Resolution to 640x400 (Default-Setting, not necessary)
Set Resolution to 960x600
Set Resolution to 1280x800
Set Controls to Mouse
Set Controls to Keyboard (Default-Setting, not necessary)
Set Controls to Joystick
Turns HighQuality-Filter on
Set Game to Fullscreen-Mode
For example: If you want to modify the Desktop-Link: Right-Click on that "Raptor - Call of the Shadows" link and choose "Properties". Then, you can add you favorite Parameters you want. (See an example in Attachment) Don't forget to replace "raptor.exe" with "rapwin.exe".
Hope it could help you...