Setting Values in INI vs HAL

Is there any reason to set the values for pins / parameters in the INI vs. the HAL?  Is using the INI simply a best practice? 

For example, this line are in the HAL file:

          setp pid.u.Pgain                            [JOINT_4]P

and this in in the INI file

          P                    = 1000.0

I assume I could set this value in the HAL file without using the INI file:

          setp pid.u.Pgain                            1000.0

 

For one, thing the "Calibration" window will not show that as a tune-able option in the calibration window.