Hi Jamie,
You are correct, as you have found the military spec exhaust is totally different to the civvy one.
I am not up to speed with the civilian type, but I think that it runs underneath the chassis, while the military one runs through the holes in the chassis cross members, much higher up and safer from damage.
The military LWB vehicles also use the SWB engine pipe, this is also different to the civilian system.
I have done the same as you, I got my exhaust bloke to modify the civvy pipe to fit the chassis. I did ask him to make me one from scratch, eventually he came back and said that he did’nt have a pipe bender that could bend the pipe at the back to go over the rear axle and then run 90 degrees around to hook up with the muffler. These 2 bends were too close to each other, so we just modified the civvy pipe to fit.
At least the muffler is the same as the civilian one!
Cheers,
Mike.