Just a thought, but since it does not occur in the 53 but does in the 39, is it possible that your chain length is not just right or the spring tension is a bit off on the RD? When you go the 39 the chain tension will definitely reduce a significant amount and it could be allowing the resonance?
According, to chain length methods, it seems the chain could be shortened a bit. Perhaps, shortening the chain length will resolve the resonance.
https://youtu.be/Vg2SoOOrpE8
There are more than one chain length method and they are all just ROUGH GUIDES to get you to a STARTING POINT.
The lengths these methods give will only give you a length that won’t rip a derailleur off or have a slack chain, and only then if you are totally within the recomended configuration for the parts you have.
If you have short chain stays, then you are out of spec and need to spend some time to find the best setup.
You need to check the configuration across the operating range and size for best operation.
The best way is use an old joiner link and size the chain for maximum length, that is when in little cog/little cog, the two pulleys just clear.the chain and apply some tension.
You can then run the system through all gears and test how it runs looking at the distance between the top pulley and cogs in all gears.
You can then play with B tension and grabbing the chain links to try shorter chain to see if the cog gap can be made small and consistent across the stack in both rings.and manipulate the deraileur with your hand to change things up if there is a problem. If some gears have a 10mm gap and others 3mm gap, then something may be better.
Once you find your perfect length, fit a new link or joiner pin as you prefer.
With short chainstay bikes like tri bikes, longer chains tend to be better as the lower chain span takes a less crossed path.
If you run shorter, the severe cross of the chain can influence how the chain runs through the pulleys and can pull the chain off line to the cogs as it twists it’s way through the deraileur cage.
This is why they have minimum chainstay lengths and one of the reasons higher cog counts are harder to engineer.
Shimano can no longer run their floating top cog due to this as the wider stack of 11 speed twists the chain on moderate crossed cogs as a narrower chain has less resistance to this, and then looses indexing.
I bet if you put a shimano cluster on there the noise goes away…