The MVP uses a lithium battery. A proper charging chip doesn't use voltage to determine when it's fully charged, but will instead offer a constant voltage to the battery, while monitoring how much current is going in. When the current going in drops to a certain level, the battery is charged, regardless of the voltage. Individual batteries will vary slightly, that method adapts to the differences. Between that, and the fact that the voltmeter isn't exact, don't worry about whether your's shows 4.1 or 4.2 V when full. It's not the voltage which determines when it's full.
Discharging a lithium battery below about 3 Volts will damage it. Lithium batteries like to be kept charged - you'll get more cycles from charging early and often than by fully draining and recharging. But you obviously don't get as much out of each cycle. So there's a balance. I think innokin sets the full dischage (red led) warning to about 3.3V - low enough that you get a lot of use out of a charge, but high enough to avoid reducing the lifetime of the battery. To get the maximum useful lifetime out of your battery, you should probably let it discharge until you get the yellow warning.
More info here.
Thank you for the explanation =)