Mine does it too, as well as many people with newer rubis, maybe even new TJs. Seems the newer ones have many new noises and quirks over the old ones
Ive also had my 6spd replaced a few times, as well as that engine noise. Dealer said noise is normal. they are pretty honest, fixed most things without a hassle, so I think it really is a "normal" noise on these new ones.
I thought it might be an exhaust leak also. Had the downpipe replaced, new gaskets, and the manifold tightened as it was hitting my front driveshaft. Noise still there.