The P, Q, R modes 'fly' the aircraft through a sinusoidal oscillation in roll, pitch, or yaw (respectively) using the time-accurate unsteady solver.
The time-history of the forces and moments through these oscillations is used to calculate the unsteady S&C derivatives that can not be calculated using the steady state calculations in the -stab mode.
I would not consider the P, Q, R analyses to be flight dynamic modeling. Instead, they help you calculate more of the stability derivatives you need to do flight dynamic modeling.
Rob