Electric Box Fill - 'Ambiguous' Conductor

I have 3 hall luminaires controlled by a 4-way switching system. The electrician elected to run 14-3/G NM too all the fixtures. The most distant one is mounted on a round 4 inch x 1/2 inch pancake box. The capacity is marked 6 cu in. The red lead is in the box, but it is capped with a wire nut and not otherwise used. Does it count for 2 cu in like the black and white leads or does it count for 1 cu in like the ground because it is 'dead.'

Here's an image. Its worth many words. As you can see, it is mounted on 2x6 tongue-and-groove redwood decking with the wiring on the opposite face of the decking, under the roof coating.



Does anyone recognize the black, plastic 'grommet' between the box and the cable? It is just above the loop in the solid ground wire. I'd like to be able to give it its proper name.

Are these acceptable under the National Electric Code in the USA?

Are the missing knockouts a violation?

The manufacturer suggests that the luminaire can be installed using only the central 1/8" IPT hole in the crossbar as long as the 1/8" nipple carries a lock washer and nut to fix it to the crossbar and a lock washer and nut secure the fixture to the nipple. Clearly the electrician had difficulty using the matching round head machine screws that can be installed in the threaded hole in the crossbar and the matching hole diagonally opposite it. Getting all 3 supports to line up is challenging.

Can I use only the nipple and meet code?

thanks

baumgrenze