The colors I listed first are the short wires in the left control's harness, right where they plug into the clutch switch. I got them from Wiring_Schematic_-_R4.pdf, but I can't personally verify they're correct. The second set of colors I listed are the main harness colors, and match up with what you said. Ignoring the few inches of different colored wire, just go with yellow/green, light green, and black/yellow respectively, which is exactly what your explanation and table show.
One thing to keep in mind is that the igniter and starter circuit relay access the safety switches differently. The green/black from the igniter runs through the diodes to the green/white (sidestand), green (neutral), and yellow/green (clutch). If any one (or more) of those is "safe" and complete to ground, the igniter will work and allow the bike to run.
So you're sitting on the running bike, ready to take off, but you left the sidestand down. It's in neutral, so the neutral switch is closed and the igniter works. You pull the clutch and put it in gear. The neutral switch is now open, but the clutch switch (to ground) is closed, so the igniter still works. As you release the clutch lever, the clutch switch opens and the igniter no longer works, killing the engine. Once you have the sidestand up, its switch closes to ground and the igniter keeps working, allowing you to do whatever you want with the clutch lever and gear shifter (which is really handy when you're riding).
However, the starter circuit relay is tied directly into the yellow/green wire after the diode. The clutch switch is the only thing that can ground it and allow the starter to work. When you pull the clutch lever, the switch bridges to the black/yellow ground wire and completes the circuit directly. Regardless of the position of the other two switches, the bike will start and run. If you release the clutch lever, the switch bridges to a fork of the green wire from the neutral switch. If you have the clutch released, the bike needs to be in neutral to complete the circuit to ground and start. You need either clutch or neutral for the starter to work (and it's complicated somewhat by the neutral wire passing through the clutch switch).
If you unplug the 3-pin connector from the clutch switch, the starter button will be completely dead, because the relay can't ground due to the "broken" yellow/green wire. If you remove the green wire from the clutch switch (should be black/red right at the connector according to the PDF), the bike won't start in neutral (the neutral light will still be on even) with the clutch released. The starter circuit doesn't touch the sidestand switch at all.
The NewGen is wired differently. They ran the green neutral wire through Diode A into the yellow/green wire without going through the clutch switch. It looks like they kept the dual-throw switch, but nothing is hooked up to the "neutral switch" contact, so it acts like a single-throw. They've replaced the black/yellow direct ground with a fork of the green/white to the sidestand switch. On the NewGen, the "it'll start and run as long as the clutch is pulled" line only applies if the sidestand is also up.
The old setup kept the bike from running if you left the sidestand down, but there might have been a bit of movement, depending on exactly when the clutch switch opened and when the clutch engaged. That's the only reason I can think of for having the clutch switch tie into the sidestand rather than using a direct ground - you need to have the sidestand up (implying that you're on the bike) in order for holding the clutch to work, meaning it's not a big deal if the bike jerks an inch before dying. That little jerk might be enough to knock it off the sidestand if you weren't on the bike.