I know the kits supply 'add-on' wires for those from the Alternator as that is the easiest way to get people to fit them and I'm sure plenty of people have done it that way without issue but that doesn't really get over the fact the wires are too small and ideally ought to be a larger cross section.
But think about it, I'm sure they wouldn't sell half as many kits if people had to remove the engine case and fit new wires to the Stator.
Here's a good read on the subject if you feel like it.
http://www.ducati-upnorth.com/tech/chargingfailure.php