Well the mod slot is no longer a universal all ship slot anymore. 2nd edition changed that.
So quick history even though most already know this but for those that are newer here it goes. So 1st edition X-wing was a table top game that used printed cards for list building. Different pilot cards had different slots in the upgrade bar saying which type of upgrade could be attached. Each upgrade had to have a matching slot to its type to be attached to the pilot. So take your lowly Academy Pilot which had no upgrade slots, means you cannot attach any upgrades to it, so you are only left with the stock model.
Now in the second wave (1st edition) they added two new upgrade types. Modifications and Titles. Now instead of leaving out Wave 1 and Core out like most new upgrade slots, a Rules supplement was given that said every pilot now has a modification slot and a title slot without needing the new upgrade slot printed on it. Thus now even your lowly Academy Pilot has an option to Trick-Up Their Ride. Later those slots were often used as a fix to ships that happen to be behind the power curve.
Now with 2nd edition modifications slots is just another type of upgrade slot. It is no different than system, tech, or illicit other than what group they are in.