How is the -3.3VA voltage in this circuit generated
So the MT3608 is a boost converter. The square wave at SW goes from one diode drop below ground to one diode drop above 3.3V (enforced by the feedback loop). So the swing is 3.3V plus two diode drops.
With C89 the voltage on the non-SW side of it cannot go higher than GND + one diode drop (because of D20) when the SW pin goes to + 3.3 + Vf, so when the SW pin goes to -Vf the other side of C89 will go to -(3.3V + Vf) and thus the voltage on the other side of D21 will be -3.3V.
Since the diode drops vary with current, the voltage on the negative output will tend to be more or less than the regulated +3.3V output, depending on the relative loading of the outputs.