Does a 2.1 Amp charger harm Iphone?

You didn't control for other factors that affect charging time, such as background processes, messages received, notifications, email received, how long the screen was on, screen brightness (which may vary if auto brightness is on) etc while charging. Any activity on the phone will affect charging time. A USB adapter that can supply at least 1.5 amps will charge an iPhone slightly faster than the 1 amp cube, everything else being equal. But it won't be a big difference.

But follow Meg's advice also.

Is this a Made for iPhone certified adapter? If not, I'd avoid using it.

I primarily use iPad chargers for both my iPhones and iPads. Apple sells the same charger as fit for both.