Well, T-Cro would be the one to know for sure. He'll probably be along shortly.
Thinking a little about it, (And without consulting a wiring diagram) it might matter. Since I think the wire in question is the one that senses the "speed" of the bike. (Actually senses the RPM by reading the voltage off the coils) If all four stick coils go through one ground wire, it might make a difference to what the cruise control "sees". If it does, then changing the DIP switches on the cruise control would correct this. (Though I don't know what changes would have to be made)
Yeah, not the most helpful answer, but someone with more/better knowledge will surely be along soon.