I did some tests by re-exporting your game and from what I found out is that the flash happens when you build it with Crosswalk.
With the splashscreen plugin installed in XDK and built without Crosswalk the game would start up with the default Cordova splash screen (I didn't bother to replace the images) and it pulses for a while (for a few seconds, till it loads) then it simply fades to your loading layout. I suggest try a build with this method.