Each fuel jet is essentially in a tube, sort of like a straw with a pinched section. A straw functions based on a pressure differential. The volume of material drawn through the straw can be regulated by how much pressure differential is applied to the straw ends, as well as how much the tube is pinched.
PODs shorten the inlet duct, which raises the carb throat pressure at the outlet of the jet tube(straw). The inlet of the jet tube has the same old pressure applied to it, which is outside atmospheric pressure (the stack of air pulled by gravity from the planet's surface to outer space), both before and after POD installation. Since the pressure differential applied to the jet tube was changed with PODs, to return to the same jet fuel flow as prior to change, the jet orifice must be enlarged (like reducing the amount of pinch in the soda straw).
The pilot jet has an adjustment (air bleed) that provides some regulation to the outside atmospheric pressure reaching the jet tube outlet. However, the range of adjustment available may be too narrow to provide full restoration of pilot jet fuel flow after pods are installed. So, the jet must be changed in this case. Since these carbs are supposed to run rich at idle to provide throttle response from idle under load, if the bike stumbles in this regime, and the air bleed screw adjustment can't correct it, then a larger pilot jet is indicated.
Another answer is:
Jet changes are punishment for putting cheap ugly exposed filters on your bike, and making the whole process more expensive in time and materials than what was originally on the bike.
Cheers,