the GRA weapons can have GRA mods added to em. Kinda stupid if you ask me, shoulda just added the new modifications for normal weapons.
This is what Josh tried to do, but in the end, because of limitations (and a lack of foresight) they had to do it the way they did. Because the new mods were introduced in a dlc, there was a potential for load order bugs. It was a fairly small potential, but if one happened, it completely screwed the pooch, game unpalyable, saves corrupted, meteor showers and Justin Beiber elected as President kinda bad. Rather than risk yet another dlc release that had the potential for game breaking bugs, they went the less risky route of just adding the GRA versions along with the mods. All GRA version of weapon are exactly the same, with the exception of the GRA AMR, which (I believe accidently) has a higher AP cost than the most recently patched main game version. Also, since all these weapons were introduced by DLC, they also can't be added (again, due to poor foresight) to any perks that were introduced by other DLCs. So you get a weird scenario where the base game Assualt Carbine gets the damage boost from the Grunt perk, while the Assault Carbine (GRA) doesn't, but has a higher rate of fire with the Light Bolt mod attached. Which one's better? That's subjective, but the numbers suggest the regular one with Grunt is best. It has 3 more damage than the GRA one and a base DPS 8 higher.
I hope this explains the reasons why Josh had to do it the way they did.
-Gunny