A 20,000 cell problem is a pretty small problem. A rule of thumb is parallel simulations are not practical unless the number of cells is at least 100,000 to 1,000,000. The number of stress periods doesn't really figure into parallel performance since a single time step is solved before proceeding to the next time step, just like serial simulations.
The only fair parallel runtime comparison is running the model on 1 core with the PETSc solver. Although IMS and PETSc implement the same Krylov solvers the implementation in each is slightly different. Also, IMS has been tuned over the years for groundwater problems (incorporating many of the best options from PCG2 and xMD).