I had a look at the file and I think the main issue is the dimensions of the FDTD region. If we look at your simulation:
The way it is set, you are modelling a periodic distribution of pillars, as there is a gap between the object and the FDTD periodic boundaries. To model the structure as intended (different layers extending in the xy plane), you just need to have the FDTD region to be the size of the unit cell you want to model. Without particle in the Si, the width of the FDTD region can be arbitrary, but when you add the particle, then the size of the FDTD region will define the period of your structure.
Note that you can extend the structure through the limit of the simulation region, it doesn’t matter.
Another point, you are using the “solar_generation” analysis group to calculate the absorption. The group covers the Si3N4 and Al layers. To get the absorption in Si only, you should set its dimension to the thickness of the Si layer only.
Also, as a start, you can use a coarse mesh so the simulations are faster.