If you think about a manual transmission mechanically, different things are happening when clutch is in versus released, so therefore it's obviously going to sound different.
My 2012 6 speed sounds the same, and I believe it to be normal.
The 2012 6 speed that I test drove before I bought mine sounded the same as well.
The previous TJ's I've had also sounded this way.
So did my YJ.
Start the engine, tranny in neutral, clutch out, and turn your AC on(so the compressor runs).
That noise get's louder, doesn't it?
Start the engine, tranny in neutral, clutch out, push up on shifter and it stops(yes, I know you covered this already...just follow me). Normal.
Start the engine, tranny in neutral, clutch out, BE IN LOW RANGE, push up on shifter and your Jeep will creep forward. Normal.
It's normal. Every one does it.
If you say yours doesn't, come to Columbus Ohio and let me listen.
If it doesn't do it, I'll pay your Jeep off.
2012 Jeep Wrangler Unlimited Rubicon
Stock, for now...