The answer to your first question is yes. It is definitely possible for one high-energy photon to be absorbed by Si substrate and create multiple electron-hole pairs (ehps) (check out this article). However, for most materials (including Si), the probability of this happening is very small. In most cases, when a high energy photon gets absorbed, only one ehp is generated where the electron initially sits at an energy level that is way above the conduction band minima. The electron then releases its excess energy as thermal energy and goes to the lowest available energy levels. In special cases, special structures (or materials) can be created that uses quantum confinements (e.g. quantum dots) to increase the probability of multiple ehp generation from single high-energy photon. In such cases this effect can no longer be neglected. However, for most solar cells, the probability of multiple ehp generation is negligible and does not need to be considered in the simulation.
The solar cell application examples on our KB neglects multiple ehp generation and assumes single ehp generation for each absorbed photon (which is justified as discussed above). This calculation is done inside FDTD Solutions as a post-process using the solar cell analysis group. However, since in most cases the system can be assumed linear, in theory, this post-calculation can be adjusted to account for multiple ehp generation for high energy photons. The users will have to determine what mode (equation) is suitable for their device of interest and implement it in the calculation of ehp generation.