A Microcontroller Amplifer (theory)

No, the ADC is 10 bits.
Standard PWM out is 8 bits, but 16 bit PWM is supported by the hardware.
He didn't say what kind of amplification - voltage or current.
Aref can be adjusted - if incoming signal is 0-1V, then Aref at 1.1V will allow full 10-bit resoution. If Aref was at 5V, then a smaller range would result as you suggest.