That will be fixed with the auto config feature I'm adding to the emu's. Just set the configuration the way you want it, turn "auto config" to on and all games that does not have a configuration will use your settings.
Tell you what... Help me get blarrg's NTSC filter working in Mednafenx_NES and you can do the synopsis code.

I could send you mine if need be, although it is geared towards x-port's frontend. Plus it could probably use a little bit of cleaning up.
Actually it doesn't really matter to me... But if you could get a "proof of concept" working in MednafenX_NES I'd be grateful. I have my hands a bit full with everything else right now. Trying to meet that march deadline..