Game mechanics -wise that was propably done to avoid bugs. The non-unique GRA weapons are exactly the same as the non-GRA ones, with the exception that they can be modified.
Yeah, it's a load order issue, they had to make duplicate GRA version weapon sets to make the mods work with them.
GRA ammo (both hand loaded and purchased) however, can be used on all weapons such as the 12ga Dragonbreath and Flechette Rounds and the 20mm and 40mm Plasma Grenade Rounds.
IIRC the exception is the vanilla Fatman, the GRA mini-nukes will only work with the GRA Fatman and Esther.