Joe,
I consider it a violation of several articles, not the least of which is 110-3 which is how materials are to be utlilized.
The conductors are fire alarm conductors, and fire and security conductors are included in the box.
The disparate bonds are what concerns me the most. Should a fault occur on either the pipe, or the box, there would quite likely be a sizable arc to the item not securely fastened.
Walrus, did you forget to bring your bender with you to go around the box instead of through it? I don't understand. I have also shielded intrinsically safe conductors, but also managed to use connectors for a solid grounding connection or went around the offending item in the way.
Accessibility is one of the issues brought to the contractors attention.