Actually, that rattle is not the TOB. The rattle exists on pretty much every manual Wrangler I have been around 13 and 14's in particular. The TOB is going bad when you have a "rusty spring" creaking noise when you are pressing the clutch pedal in about mid-stroke. The noise comes right from the tranny itself, but is loud enough to be heard/felt when pulling into the driveway or garage with the windows up. Another indicator of a TOB issue is a small squealing noise coming from the same area when the clutch pedal is up. As soon as you even slightly press the pedal, the noise goes away.
My 13 went in the shop 2 months ago for the TOB, which was found to be bad and replaced under warranty. It made the noise again a month later, went back, and again it was replaced. As soon as I drove it away, I started hearing the squeal (which almost sounded like a water pump bearing going bad--which I also had replaced under warranty). It has been back in the shop since Tuesday, and they are tearing it down to try to fix the issue once and for all...especially since my warranty is up in 5 days.
The rattle (almost like a diesel sound) is present in my buddies 14 JK as well, and it seems to me like that is just truly "a Jeep thing".