If I get the Anti-Material Rifle(GRA) from the Gun Runners, trick it out with all the accessories (the Anti-materiel rifle custom bolt, the Anti-materiel rifle suppressor, and the Anti-materiel rifle carbon fiber parts) and then give it and some .50 cal bullets to Boone, then when Boone equips it it looks and acts just like it's a stock AMR. That is, the gun-stock looks wooden instead of carbon-fibre, the custom bolt does not appear to be there, the sound suppressor appears to be missing from the end of the gun barrel, and it makes the full-noise sound instead of the suppressed sound. Is this a bug with the rifle, a bug with Boone, or are all the NPCs not capable of using modified guns?

That's how they all work, if I remember correct.

You could give Boone a modded sniper rifle with a silencer and that wouldn't work either. It has to do with mods, not the GRA DLC.

Yep you have to give them uniques like the Christiens sniper rifle that have the mods 'built in' for them to work.