I think the switches are usually general purpose, with provision for some extra functions. Your machine has the most basic wiring arrangement that I have seen on any decent machine - and I see that as a good thing generally. (I'd have more safety switches, but that is a personal view.)
If the two unused wires are bound together, and if your machine is missing the hour meter, I'd guess that is the explanation.
Your feeble little alternator probably does charge the battery slightly, they don't often fail. You can check by putting a 10 Amp ammeter between the engine's output wire (red) and the mower's battery charging wire (orange). You should see a current into the battery when the engine is running at maximum speed, and zero current when the engine is stopped. If you get less than a third of an Amp of current, most likely the diode in the red (engine side) lead will have failed, but it doesn't happen all that often.
