If you buy an armor, remove all the plating and install new Superior plating, you effectively have a new Superior armor that should have the same "customization slots" of the original armor.
Unless it's the plating with the hardpoints you are replacing with lighter aftermarket stuff to conserve weight.
Even the H7 Equalizer Blaster Pistol (Suns of Fortune) is exactly a Superior Blaster Pistol, but it has 3 Hard Points (as a standard Blaster Pisotol).
Thats how the game works. The stock stuff in the rule book it the generic base representation of gear you'd find the galaxy over. So if an item's make and model needs to be called out and statted, it's probably because it's different enough to warrant it. Be it because the item is better, or because it's total garbage.
If you switch to you "Mods use up no hard points" method, not only to you cause problems for the player who like to customize his gear to fit each adventure, but you also start stepping on the toes of that special kit that's out there.
If my TaggeMart store brand heavy battle armor can, without using up hardpoints, be modded to match Mandalorian armor's base stats, why should I ever want Mandalorian armor?