A1: CHARGE only solves charge transportation. It does not simulate the optical frequency response of absorption. In the example, it mentions in Step 2: "After running a single CHARGE/MQW coupled simulation, absorption is automatically calculated at different bias points. The absorption coefficients and perturbation to the real part of the refractive index for TE and TM modes are plotted. The transmission for the TE mode is then calculated and compared with the literature. " So it is the MQW that calculates the absorption.
A2: I an not sure what does "the absorption spectra were also distorted" how to define the distortion and what is the reference here?
As long as the optical and electrical properties of the materials, and structures are correct, with proper meshing the simulation result should be correct. You may need some time for the example.