Unproven BS guess at what the Yamma engineers were doing.... The spring clip just causes a little preload to be kept on that first friction plate which is different than the main clutch pack (set of 7), but similar to the friction plate at the pressure plate end. So, at each end of the sandwich, we have different friction plates which may act as dampers. These two plates are the first points of contact when the clutch is engaged. This may smooth out the clutch engagement..... YCC-S may already be preloaded, or not, depending if in that situation they want the first friction plate free to disengage fully (perhaps to have as many plates disengaged as possible).
I'd just make another wild guess that leaving the wire out won't have any real detrimental effects. I could see a small upside by having another plate disengage when you pull in the clutch lever......
The kerchunk is simply a matter of non-syncro trannie shaft still spinning while clutch disengaged, something that will never really get resolved without significant design change. Since it's a wet clutch (odd, as we know it's not really all that wet, LOL), the oil film will prevent absolute full disengagement when you pull in the clutch lever (other minor factors at play too, but KISS). Naturally worse when cold with oil at higher viscosity.