Noises are always so much fun to diagnose virtually.

Some thoughts:

-bad engine mounts. When failing, they can transmit drivetrain noise through the chassis into the cabin. When in reverse, there is a change in torque-loading, which could find just enough flex in the mount to carry sound. On the M54 they're hydraulic IIRC, which would explain the temperature dependence. They can fail absolutely, and when they do, the engine drops. Because the starboard drive axle passes through the sump, that doesn't end well.

-low, or old, rear differential fluid. It is marginally air-cooled, and un-filtered, and doesn't hold much (1-1.5 quarts). A little seepage over time can lower the fluid level, leaving less fluid to absorb heat, cooking it further, thinning it out, hastening the leak... it's a viscous cycle.

-worn CSB, giubo, or failing u-joints. Listen for an audible "tink" when placed in gear (especially if raised to a high idle), and look for orange dust around the u-joint trunnion. Dust = rust = needs replacement, possibly of the entire shaft. If allowed to seize, the shaft itself my bend. M54 shafts have joints that are easier to replace than N52 cars due to shape of the yoke. Shafts turn opposite in reverse, so again, different torque loading.

-broken/rust parking brake shoes. They're inside the rear rotor hats (essentially drum brakes) and I've seen drums make noise uni-directionally when they get disgusting inside. Verify by jacking up, placing car in neutral, and spinning a wheel back and forth.

-old transmission fluid. GM says to change it every 45k miles (they made the transmission). If you did a simple drain/fill, only 1/3 of the fluid was changed anyway; 2/3 dates to the previous drain/fill, with 2/3 of that from the one before that, etc. It may not solve your issue, but as it's due anyway, I'd start with another couple of drain/fills separated by 50-100 miles each, and a bottle of Lubegard Red on the final fill; LG does make a difference.

Beyond that, there's any number of possible sources of noise/clunking; every part that move, and even some that don't, are a possible source. Shocks, sway bars, thrust arms, loose subframe, loose stiffener plate/splash shields, struts.

 

Dukedkt442: Exceptional reply! Thanks for taking the time to give such a thorough response. Was expecting the new transfer case mount to cure my problems, but was disappointed to see no improvement. Will crawl under the car once again this weekend to see if I can spot anything obvious. Will be having an independent shop take a look at it on Wednesday (same shop that competently replaced the A/C evaporator at the beginning of the summer).
I did replace fluid in both differentials at the same time I did the transmission fluid & filter so I'm not sure they're the problem. Did the rear brakes last year & feel confident they're not the problem as the noise happens when, at a standstill, the selector is simply changed from D to R. Taking it out of R into D or N eliminates the noise.
Hopefully, once that's sorted, the clunk going over rough roads will be eliminated... surely I can't be unlucky enough to have two things go wrong at the same time!
Thanks again for taking the time to reply. Will be giving a copy of your thoughts to the mechanic on Wednesday to help him check out a few possibilities.

 

Dukedkt442: Exceptional reply! Thanks for taking the time to give such a thorough response. Was expecting the new transfer case mount to cure my problems, but was disappointed to see no improvement. Will crawl under the car once again this weekend to see if I can spot anything obvious. Will be having an independent shop take a look at it on Wednesday (same shop that competently replaced the A/C evaporator at the beginning of the summer). I did replace fluid in both differentials at the same time I did the transmission fluid & filter so I'm not sure they're the problem. Did the rear brakes last year & feel confident they're not the problem as the noise happens when, at a standstill, the selector is simply changed from D to R. Taking it out of R into D or N eliminates the noise. Hopefully, once that's sorted, the clunk going over rough roads will be eliminated... surely I can't be unlucky enough to have two things go wrong at the same time! Thanks again for taking the time to reply. Will be giving a copy of your thoughts to the mechanic on Wednesday to help him check out a few possibilities.

I am experiencing a very similar issue when the engine is cold, and shifting into reverse. Did you ever figure out what the problem was? Thanks.

 

Yes.
The first mechanic said the transmission mount was bad, so I had that replaced. Although in looking at the old one, it certainly needed replacing, but that turned out not to be the case. Took it to another independent shop, and they found that where the control arm attaches to the engine, the bolt(s) were sheared off and the engine had dropped down. Every time I hit a patch of rough road, a vicious klunk was heard. Had to remove the intake manifold, then extract from the engine what was left of the bolts to reattach the suspension. Fixed!
Your problem sounds different from mine. Mine could be heard as a loud knock whenever I went over rough road, weather warm or cold.... forward or reverse. Must be something different for you.
Are you sure you're not hearing the motor from the right hand rear view mirror moving when you put the car into reverse? That threw me once until I figured out what that noise was... Good luck!

 

Engine mount(s), not control arm.